Drosophila mature starts 45? 1 mslslllrga vrcnaanlvk saritplksy stlvanvqrk avvqplavak ivapvvreis 61 vsaprmasag sshtllwtve rivsagllav ipaafiapsq vldalmaisv vihthwgvea 121 mvvdymrpsv vgnvlpkvah ialiiisvat lgglfyfiqn dvglangikr fwaikgkdae 181 ka
Somewhat ambguous- hydropathy, hydro-moment plot might help.N-term in insects and nematodes is OKIn some may be leader peptide.Asuumx3 MLSAVRRAIPLSARILRTSLIQRCAGA Celegans MAASLRHMAHFQKALLVA Asperg.o. MASIARQSSLLRQSCLSAFRSPFATRNGAGVSQVVAFHA 10 20 30 | | | | * | |Humanx2 --------------------------SGSKAASLHWTSERVVSVLLLGLLPAAYLNP QPSbov --------------------------SGSKAASLHWTGERVVSVLLLGLIPAAYLNP Gallus --------------------------GSSKAASLHWTSERAVSALLLGLLPAAYLYP Droso ---PLAVAKIVAPVVREISVSAPRMASAGSSHTLLWTVERIVSAGLLAVIPAAFIAP Asuumx3 ----TSAAVTGAAPPQFDPIAAEKGFKPLHSHGTLFKIERYFAAAMVPLIPAAYFIH Celegans ---RSAPRISTIVRATSTLNDGNDGASKVPDHSMHFKLERLWAVGMLPILPASYFIHSacchcere LTIPFLPVLPQKPGGVRGTPNDAYVPPPENKLSYHWYMEKIFALSVVPLATTAMLTTGPL Asperg.o. SAKKQILPPLPQTIQGTMNDPAPIPTPHPSEGSYHWTFERAISAGLVPLTIAPFAAGChondrus MITFQWLIVRVVALFISLTILIDI Porphyra MYKTLLAQVFFHSIAKKKLYFFWL-PRLFSLLLVPGFLFDI S.lycopersicum MKEGISGLRNESSKTKRTGLFQRITAAFLLPLIIIYK Rrubrum MSLRSPLGRARRGFRQGGAANHWMAERLPAIALVPLALWFVFV-- Reclinomonas MTEKLLHFIRTKSGSMHWWLQRFLAILLAPIILYLLFD parden MRYITPRKAAEGLGSAHEGTQHHWAMTVSAVALTVLTPLFMIVV Brady MSATDTPKRSMRTPLGRVRNLGAAHSGTSDFWRQRITGVAMVLMMIPVIVI--- EcoliSDH --------------------MVSNASALGRNGVHDFILVRATAIVLTLYIIYMVGEGF Woli MTNESILESYSGVTPERKKSRMPAKLDWWQSATGLFLGLFMIGHMFFVSTILL ??? TMHelix 1 30 40 50 60 | | | * | ** | Humanx2 ----------------------CSAMDYSLAAALTLHGHWGLGQVVTDYVHQPSbov ----------------------CSAMDYSLAATLTLHSHWGIGQVVTDYVHGallus ----------------------GPAVDYSLAAALTLHGHWGLGQVITDYVHDroso -----------------------SQVLDALMAISVVIHTHWGVEAMVVDYMR Asuumx3 ----------------------GREMDLCLALALTLHVHWGVWGVVNDYGR Celegans ----------------------GPVMDAVLTVALTLHIHWGIHGVVYDYAR Sacchcere ----------------------STAADSFFSVMLLGYCYMEFNSCITDYIS Asperg.o ------------- -------SLNMDAVLCSFIVLHSHIGFQAAIIDYFPChondrus ------------------------EMFVVMLSFLIIHISIGLKAIIHDYIH Porphyra --(bact linker helix)---EILFLFHPIILLHASLGLSVIIEDYIH S.lycopersicum KVSSTFLLNLSLFWHINEGIEEIMADYVH Rrubrum AIISNLGASYAQIQAFMAVPLNATLMLLTVFCAFFHGALGLIVIIEDYVQ Reclinomona VAIYIGQQSDPTVMMFLNRIFNHNSIFIFITSVILIWHVRGGMEVIIEDYVH parden ARAIGLSQEQLLAYFGRPFPALITA---LFVIVGMVHFIKGTRIMIDDYFQ--Bradyx9 IVMLFGRNQAFVAQTIGSLPIAIIMLLFIFASAWHMKIGMQVVIEDYVH EcoliSDH PVFATSGELTYEVWIGFFASAFTKVFTLLALFSILIHAWIGMWQVLTDYVKWoli GDNVMLWVTKKFELDFIFEGGKPIVVSFLAAFVFAVFIAHAFLAMRKFPINYRQY bact linker helix TMHelix 2 70 80 90 100 110 | | | |Humanx2 ---GDALQKAAKAGLLALSALTFAGLCYFNYHDVGICKAVAMLWKLQPSbov ---GDAVQKAAKTGLLVLSAFTFAGLCYFNYHDVGICKAVAMLWKLGallus ---GDTPIKVANTGLYVLSAITFTGLCYFNYYDVGICKAVAMLWSI TGL:G82 pocket where C:L61 insertsDroso PSVVGNVLPKVAHIALIIISVATLGGLFYFIQNDVGLANGIKRFWAIKGKDAEKAAsuumx3 PFVLGDTLAAAVRVGAYIFTACLLAGLLYFNEHDVGLTRAFEMVWEL--- Celegans PYVIGEAAAKAAHVGVYLITGLLLGALLHFNTNDVGITKAFELVFSL--- Sacchcere ERVYGVWHKYAMYMLGLGSAVSLFGIYKLETENDGVVGLVKSLWDSSEKDNSQKIEAKKAsperg.o. TRRVPKTATFCNWLLRAFTLTTAVGLYEFETNDVGVTEAFKRVWKA Chondrus FQKIKLMLLILLRVSAIEISRSFRTFYIIIKNT-- Porphyra IETIKFQYLSLIKLLLVLLINLNILYLL--- S.lycopersicum QEMTRNWILVYLRLFLLIVIKDVFLSLVFFLKKK Rrubrum NHAVKNALVFGTKLYALFGAVLAAVSILKLTFGG Reclinomonas GEKTRIVSIFLIRVIAIEIMEYLYKCSIIF----- paradeni GGTRKVAIIFSVIFGWAVIAAAVYALARMGLGAIVVLBradyx9 NEKLKLTAIMLNNFFSIAVALASTYAILKLSSGV EcoliSDH ---PLALRLMLQLVIVVALVVYVIYGFVVVWG based on structureWoli LTF<helix 3 omitted> TMHelix 3 Vert CTHelix ------------------------------- ----------
Somewhat ambguous- hydropathy, hydro-moment plot might help.N-term in insects and nematodes is OKIn some may be leader peptide.Asuumx3 MLSAVRRAIPLSARILRTSLI
QR
CAGA
Celegans MAASLRHMAHFQKALLVA
Asperg.o. MASIARQSSLLRQSCLSAFRSPFATRNGAGVSQVVAFHA
10 20 30 | | | | * | |Humanx2 --------------------------SGSK
AASLHWTSERVVSVLLLGLLPAAYL
N
P
QPSbov --------------------------SGSK
AASLHWTGERVVSVLLLGLIPAAYL
Gallus
--------------------------GSSK
AASLHWTSERAVSALLLGLLPAAYL
Y
Droso ---PLAVAKIVAPVVREISVSAPRMASAGSSHTLLWTVERIVSAGLLAVIPAAFIAP
Droso ---
PLAVAKIVAPVVREISVSAPRMASAGSSHTLLWTVERIVSAGLLAVIPAAFIAP
Asuumx3 ----TSAAVTGAAPPQFDPIAAEKG
FKPLHSHGTLFKIERYFAAAMVPLIPAAYFIH
Celegans ---
RSA
PRISTIVRATSTLNDG
NDG
ASKVPDHSMHFKLERLWAVGMLPILPASYFIH
Sacchcere
LTIPFLPVLPQKPGGVRGT
PNDAYVPPPENKL
SY
HWYMEKIFALSVVPLATT
AML
T
G
PL
Asperg.o. SAKKQILPPLPQTIQGTMNDP
Asperg.o.
APIPTPHPSEGSY
HWTFE
R
AISA
GLVPLTIAPFAAG
parden MRYITPRKAAEGLGSAHEGTQHHWAMTVSAVALTVLTPLFMI
V
EcoliSDH --------------
-----
-MVSNASALGRNGVHDFILVRATAIVLTLYIIYMVG
EG
F
30 40 50 60
| |
|
*
| ** | Humanx2
----------------------
C
SAMDYSLAAALTLHGHWGLGQVVTDYVHQPSbov
---------------------
-
SAMDYSLAATLTLHSHWGIGQVVTDYVHGallus
AVDYSLAAALTLHGHWGLGQVITDYVH
Droso
-SQVLDALMAISVVIHTHWGVEAMVVDYMR Asuumx3 ----------------------GREMDLCLALALTLHVHWGVW
GVVNDYGR
Celegans ----------------------GPVMDAVLTVALTLHIHWGIH
GVVYDYAR
STAADSFFSVMLLGYC
YMEFNSCITDYI
S
Asperg.o ------------- -------
SLN
MDAVLCSFIVLHSHIGFQAAIIDYFP
Chondrus ------------------------EMFVVMLSFLIIHISIGLK
AIIHDYIH
Porphyra --(bact linker helix)---EILFLFHPIILLHASLGLS
VIIEDYIH
parden
AR
AIGLSQEQLLAYFG
RPFPALITA---
LF
VIVGMVHFIKGTRIMIDDYFQ--
EcoliSDH
PV
FATSGELTYEVWIGFFASAFTKVFT
LLALFSILIHAWIGMWQVLTDYVK
70 80 90 100 110
| | | |Humanx2
--
-G
DAL
QKAAKAG
LLA
L
SALTFAGLCYFNYHDVGICKAVAMLWKLQPSbov
GDAV
QKAAKTG
LLV
SAFTFAGLCYFNYHDVGICKAVAMLWKLGallus
GDTP
IKVANTG
LYV
SAITFTGLCYFNYYDVGICKAVAMLWSI TGL:G82 pocket where C:L61 inserts
PSVVGNVLPKVAHIALIIISVATLGGLFYFIQNDVGLANGIKRFWAIKGKDAEKA
Asuumx3 PFVLGDTLAAAVRVGAYIFTACLLAGLLYFNEHDVGLTRAFEMVWEL--- Celegans PYVIGEAAAKAAHVGVYLITGLLLGALLHFNTNDVGITKAFELVFSL---
ERV
GVW
HKYAMYMLGLGSAVSL
FGIYKLETENDGVVGLVKSLWDSSEKDNSQKIEAKK
TRRV
PKTATFCNWLLRAFTLTTAVGLYEFETNDVGVTEAFKRVWKA
Chondrus FQKIKLMLLILLRVSAIEISRSFRTFYIIIKNT-- Porphyra IETIKFQYLSLIKLLLVLLINLNILYLL---
Rrubrum NHAVKNALVFGTKLYALFGAVLAAVSILKLTFGG
Reclinomonas GEKTRIVSIFLIRVIAIEIMEYLYKCSIIF-----
paradeni
GGT
RKVAIIFSVIFGWAVIAAAVYALARMGLGAIVVL
Bradyx9 NEKLKLTAIMLNNFFSIAVALASTYAILKLSSGV
EcoliSDH ---P
LAL
RLMLQLV
IVV
AL
VVYVIYGFVVVWG
------------------------------- ----------
Here we are aligning SDHD with the first two helices of wolinella FRD, because thats what the structure aligns (and SDHC with last 3) but there is no real homolgy[Paracoccus denitrificans] MRYITPRKAAEGLGSAHEGTQHHWAMTVSAVALTVLTPLFMIVVARAIGLSQEQLLAYFGRPFPALITAL FVIVGMVHFIKGTRIMIDDYFQGGTRKVAIIFSVIFGWAVIAAAVYALARMGLGAIVVLAspergg.o SDHD AB449815: D124E 10 20 30 40 50 60 MASIARQSSL LRQSCLSAFR SPFATRNGAG VSQVVAFHAS AKKQILPPLP QTIQGTMNDP APIPTPHPSE GSYHWTFERA ISAGLVPLTI APFAAGSLNP VMDAVLCSFI VLHSHIGFQA AIIeYFPTRR VPKTATFCNW LLRAFTLTTA VGLYEFETND VGVTEAFKRV WKA -structural alignment of SDHD: 3d tmh is offset, but pretty clear D62-D88 DTP-NY E.col D87 D113 LAL-VW and this seems to ext back to 32, 57 (but with displacement in the 2-3 linker GPA/AKV>NP_054431.1 succinate dehydrogenase subunit 4 (mitochondrion) [Marchantia paleacea] MKTHRETLGHWLLQRITAAFLIPTILIANVSTLILLNILLFWHIHVGIEEILADYVHHEVTRNWILILLR VFCLIIIKYVFVFFVF 1 Human 129 2 bovine 129 3 Gallus 129 4 EcoliSDH 129 1 -- -- -- M1 2 -- -- -- V2 3 -- -- -- S3 4 -- -- -- N4 5 -- -- -- A5 6 -- -- -- S6 7 S1 S1 G1 A7 8 G2 G2 S2 L8 9 S3 S3 S3 G9 10 K4 K4 K4 R10 11 A5 A5 A5 N11 12 A6 A6 A6 G12 13 S7 S7 S7 V13 14 L8 L8 L8 H14 15 H9 H9 H9 D15 16 W10 W10 W10 F16 17 T11 T11 T11 I17 18 S12 G12 S12 L18 19 E13 E13 E13 V19 20 R14 R14 R14 R20 21 V15 V15 A15 A21 22 V16 V16 V16 T22 23 S17 S17 S17 A23 24 V18 V18 A18 I24 25 L19 L19 L19 V25 26 L20 L20 L20 L26 27 L21 L21 L21 T27 28 G22 G22 G22 L28 29 L23 L23 L23 Y29 30 L24 I24 L24 I30 31 P25 P25 P25 I31 32 A26 A26 A26 Y32 33 A27 A27 A27 M33 34 Y28 Y28 Y28 V34 35 L29 L29 L29 G35 36 N30 N30 Y30 F36 * 37 P31 P31 P31 F37 * 38 C32 C32 G32 A38 * 39 -- -- -- T39 40 -- -- -- S40 41 -- -- -- G41 42 -- -- -- E42 43 -- -- -- L43 44 -- -- -- T44 45 -- -- -- Y45 46 -- -- -- E46 47 -- -- -- V47 48 -- -- -- W48 49 -- -- -- I49 50 -- -- -- G50 51 -- -- -- F51 52 -- -- -- F52 53 -- -- -- A53 54 -- -- -- S54 55 -- -- -- A55 56 -- -- -- F56 57 -- -- -- T57 58 S33 S33 P33 K58 *Shenoy&Yu 59 A34 A34 A34 V59 *AzidoQ-labeled 60 M35 M35 V35 F60 *peptide at 61 D36 D36 D36 T61 *distal site. 62 Y37 Y37 Y37 L62 * 63 S38 S38 S38 L63 64 L39 L39 L39 A64 65 A40 A40 A40 L65 66 A41 A41 A41 F66 67 A42 T42 A42 S67 68 L43 L43 L43 I68 69 T44 T44 T44 L69 70 L45 L45 L45 I70 71 H46 H46 H46 H71 Heme Ligand 72 G47 S47 G47 A72 73 H48 H48 H48 W73 74 W49 W49 W49 I74 75 G50 G50 G50 G75 76 L51 I51 L51 M76 77 G52 G52 G52 W77 78 Q53 Q53 Q53 Q78 79 V54 V54 V54 V79 80 V55 V55 I55 L80 81 T56 T56 T56 T81 82 D57 D57 D57 D82 D88 in paradeni- carboxin resist. 83 Y58 Y58 Y58 Y83 Quinone Ligand 84 V59 V59 V59 V84 85 H60 H60 H60 K85 86 G61 G61 G61 P86 87 D62 D62 D62 L87 88 A63 A63 T63 A88 89 L64 V64 P64 L89 90 Q65 Q65 I65 R90 91 K66 K66 K66 L91 92 A67 A67 V67 M92 93 A68 A68 A68 L93 94 K69 K69 N69 Q94 95 A70 T70 T70 L95 96 G71 G71 G71 V96 97 L72 L72 L72 I97 98 L73 L73 Y73 V98 99 A74 V74 V74 V99 100 L75 L75 L75 A100 101 S76 S76 S76 L101 102 A77 A77 A77 V102 103 L78 F78 I78 V103 104 T79 T79 T79 Y104 105 F80 F80 F80 V105 106 A81 A81 T81 I106 107 G82 G82 G82 Y107 108 L83 L83 L83 G108 109 C84 C84 C84 F109 110 Y85 Y85 Y85 V110 111 F86 F86 F86 V111 112 N87 N87 N87 V112 113 Y88 Y88 Y88 W113 114 H89 H89 Y89 G114 115 D90 D90 D90 V115 116 V91 V91 V91 -- 117 G92 G92 G92 -- 118 I93 I93 I93 -- 119 C94 C94 C94 -- 120 K95 K95 K95 -- 121 A96 A96 A96 -- 122 V97 V97 V97 -- 123 A98 A98 A98 -- 124 M99 M99 M99 -- 125 L100 L100 L100 -- 126 W101 W101 W101 -- 127 K102 K102 S102 -- 128 L103 L103 I103 -- 129 104 104 104 116 >Human ------SGSKAASLHWTSERVVSVLLLGLLPAAYLNPC-------------------SAMDYSLAAALTLHGHWGLGQVVTDYVHGDALQKAAKAGLLALSALTFAGLCYFNYHDVGICKAVAMLWKL>bovine ------SGSKAASLHWTGERVVSVLLLGLIPAAYLNPC-------------------SAMDYSLAATLTLHSHWGIGQVVTDYVHGDAVQKAAKTGLLVLSAFTFAGLCYFNYHDVGICKAVAMLWKL>Gallus ------GSSKAASLHWTSERAVSALLLGLLPAAYLYPG-------------------PAVDYSLAAALTLHGHWGLGQVITDYVHGDTPIKVANTGLYVLSAITFTGLCYFNYYDVGICKAVAMLWSI>EcoliSDH MVSNASALGRNGVHDFILVRATAIVLTLYIIYMVGFFATSGELTYEVWIGFFASAFTKVFTLLALFSILIHAWIGMWQVLTDYVKPLALRLMLQLVIVVALVVYVIYGFVVVWGV------------->Human ----------------------------------SGSKAASLHWTSERVVSVLLLGLLPAAYLNPCSAMDYSLAAALTLHGHWGLGQVVTDYVHGDALQKAAKAGLLALSALTFAGLCYFNYHDVGICKAVAMLWKL>bovine ----------------------------------SGSKAASLHWTGERVVSVLLLGLIPAAYLNPCSAMDYSLAATLTLHSHWGIGQVVTDYVHGDAVQKAAKTGLLVLSAFTFAGLCYFNYHDVGICKAVAMLWKL>Gallus ----------------------------------GSSKAASLHWTSERAVSALLLGLLPAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVHGDTPIKVANTGLYVLSAITFTGLCYFNYYDVGICKAVAMLWSI>EcoliSDH MVSNASALGRNGVHDFILVRATAIVLTLYIIYMVG-----FFATSGELTYEVWIGFFASAFT---KVFTLLALFSILIHAWIGMWQVLTDYVKPLALR-------LMLQLVIVVALVVY------VIYGFVVVWGVAsperg.o SDHD AB449815: D124E 10 20 30 40 50 60 MASIARQSSL LRQSCLSAFR SPFATRNGAG VSQVVAFHAS AKKQILPPLP QTIQGTMNDP APIPTPHPSE GSYHWTFERA ISAGLVPLTI APFAAGSLNP VMDAVLCSFI VLHSHIGFQA AIIeYFPTRR VPKTATFCNW LLRAFTLTTA VGLYEFETND VGVTEAFKRV WKA