Query 003705
Match_columns 801
No_of_seqs 111 out of 121
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 04:28:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003705.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003705hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13934 ELYS: Nuclear pore co 100.0 3.3E-50 7.1E-55 411.8 21.6 222 156-449 1-226 (226)
2 PLN03077 Protein ECB2; Provisi 76.7 66 0.0014 39.7 16.2 126 302-468 326-451 (857)
3 PLN03081 pentatricopeptide (PP 76.6 1.3E+02 0.0027 36.4 18.2 25 444-468 293-317 (697)
4 PLN03077 Protein ECB2; Provisi 66.9 1.8E+02 0.004 35.9 16.9 124 302-467 427-550 (857)
5 PF10366 Vps39_1: Vacuolar sor 66.9 26 0.00056 33.1 7.6 88 407-515 13-101 (108)
6 KOG2377 Uncharacterized conser 64.8 4.4 9.6E-05 47.2 2.5 50 274-327 547-600 (657)
7 PLN03081 pentatricopeptide (PP 63.4 1.1E+02 0.0024 36.8 13.9 56 301-362 261-316 (697)
8 PF07035 Mic1: Colon cancer-as 62.6 14 0.00031 37.7 5.3 39 285-325 77-115 (167)
9 PF04053 Coatomer_WDAD: Coatom 61.9 14 0.00031 42.8 5.9 83 262-365 259-347 (443)
10 KOG2066 Vacuolar assembly/sort 60.5 34 0.00073 42.4 8.7 161 276-469 365-533 (846)
11 PF04840 Vps16_C: Vps16, C-ter 58.0 1.4E+02 0.003 33.4 12.5 94 254-363 195-289 (319)
12 PRK11788 tetratricopeptide rep 54.7 2.7E+02 0.0059 30.1 13.9 86 271-362 73-167 (389)
13 PLN03218 maturation of RBCL 1; 51.9 2.5E+02 0.0054 36.5 14.8 54 302-361 409-462 (1060)
14 PLN03218 maturation of RBCL 1; 50.5 1.9E+02 0.0041 37.5 13.5 56 303-361 476-532 (1060)
15 PRK10049 pgaA outer membrane p 48.8 3E+02 0.0065 34.0 14.4 175 253-468 255-454 (765)
16 PF05405 Mt_ATP-synt_B: Mitoch 48.7 2E+02 0.0043 28.6 10.8 55 18-72 35-89 (163)
17 KOG1920 IkappaB kinase complex 40.8 3.2E+02 0.007 35.9 13.0 218 258-538 883-1118(1265)
18 TIGR02917 PEP_TPR_lipo putativ 38.3 5.2E+02 0.011 30.4 13.7 42 424-468 179-220 (899)
19 KOG0276 Vesicle coat complex C 36.8 2.8E+02 0.006 34.3 11.0 69 281-366 599-667 (794)
20 PF10191 COG7: Golgi complex c 36.2 1.6E+02 0.0034 36.8 9.5 124 32-170 133-265 (766)
21 TIGR02917 PEP_TPR_lipo putativ 34.0 7.4E+02 0.016 29.1 14.0 105 252-362 278-389 (899)
22 TIGR00990 3a0801s09 mitochondr 33.2 6.7E+02 0.014 29.8 13.7 23 446-468 547-569 (615)
23 KOG4182 Uncharacterized conser 31.4 1.6E+02 0.0035 35.2 7.9 92 29-131 134-232 (828)
24 KOG0547 Translocase of outer m 31.3 1.6E+02 0.0035 35.3 7.9 58 445-509 541-600 (606)
25 PRK12370 invasion protein regu 30.8 7E+02 0.015 29.5 13.3 176 251-467 277-467 (553)
26 PRK11447 cellulose synthase su 30.3 5.8E+02 0.013 33.1 13.4 82 273-362 467-555 (1157)
27 PRK10049 pgaA outer membrane p 29.7 1.1E+03 0.023 29.3 15.0 103 251-362 65-176 (765)
28 PF13429 TPR_15: Tetratricopep 29.3 56 0.0012 34.3 3.6 109 251-363 162-275 (280)
29 KOG2041 WD40 repeat protein [G 26.9 8.9E+02 0.019 30.8 13.0 93 262-362 819-936 (1189)
30 PF10293 DUF2405: Domain of un 26.7 1E+02 0.0022 31.1 4.8 33 33-65 119-151 (157)
31 PF09976 TPR_21: Tetratricopep 26.6 3.2E+02 0.007 26.0 8.0 98 255-359 34-141 (145)
32 PF13374 TPR_10: Tetratricopep 25.8 84 0.0018 22.8 3.1 30 446-475 7-36 (42)
33 PRK11447 cellulose synthase su 25.5 9.2E+02 0.02 31.4 14.0 73 251-325 128-207 (1157)
34 PRK15174 Vi polysaccharide exp 25.2 1.2E+03 0.026 28.3 14.2 103 252-362 93-203 (656)
35 PRK09782 bacteriophage N4 rece 23.4 1.7E+03 0.038 28.9 15.7 100 256-362 462-568 (987)
36 PF09098 Dehyd-heme_bind: Quin 22.4 57 0.0012 33.6 2.1 36 409-444 41-76 (167)
37 COG4755 Uncharacterized protei 22.2 8.3E+02 0.018 24.7 12.6 79 48-126 44-139 (151)
38 PF13429 TPR_15: Tetratricopep 22.1 7.5E+02 0.016 25.9 10.4 190 235-468 46-241 (280)
39 KOG2180 Late Golgi protein sor 21.6 7.1E+02 0.015 31.4 11.0 16 98-113 229-244 (793)
40 KOG4521 Nuclear pore complex, 21.5 1.2E+03 0.026 31.3 13.2 136 302-467 986-1128(1480)
41 KOG2280 Vacuolar assembly/sort 21.5 4.7E+02 0.01 33.0 9.6 93 255-363 703-797 (829)
42 TIGR02521 type_IV_pilW type IV 21.3 7.1E+02 0.015 23.6 11.6 59 301-363 67-126 (234)
No 1
>PF13934 ELYS: Nuclear pore complex assembly
Probab=100.00 E-value=3.3e-50 Score=411.81 Aligned_cols=222 Identities=36% Similarity=0.531 Sum_probs=200.3
Q ss_pred CcchHHHHHHhhchhhhhhccCCccccccccccCCCCCcccccccCCCccCCCCcc---HHHHHHHHhccCCChhhhhhH
Q 003705 156 GSLFIEDALANLEIEQEFTQGRGEELDITSLHKDDEGSSFVRSKIEGVSGCYPFEN---LRAAVDILFLHGSSDLVLAKQ 232 (801)
Q Consensus 156 g~LFID~LL~~Lgi~~~~~~~~ge~~el~~Lw~~~~~~l~f~~~~e~~t~~YPPkS---L~aLl~llfl~~ssd~~~~Kq 232 (801)
|.||||++|+++|++ +.++.|||+| |++|++.|+++++++ ++||
T Consensus 1 ~~LfiD~lL~~~gi~-------------------------------~~~~~YPP~s~~~L~~Ll~~i~~~~~~~--~~K~ 47 (226)
T PF13934_consen 1 GCLFIDRLLSRLGIE-------------------------------GSTGLYPPKSDNDLRALLDLILSSNVSL--LKKH 47 (226)
T ss_pred CcchHHHHHHHcCCC-------------------------------CCCCCCCccCHHHHHHHHHHHhcCCcCH--HHhH
Confidence 689999999998774 2469999999 999999999999987 7999
Q ss_pred HHHHHhhhccCCCCCCchhhhHHHHHHhHhCCChhhHHHHhHhhhccCCCcHHHHHHhhhCCCCCC-CCChHHHHHHHHc
Q 003705 233 AIFLYYLFDRHWTMPDENWRHIVDDFAATFSITRHSLLESLTFYLLDDQADEALQEACHLLPEISG-PTTHPKIAQVLLE 311 (801)
Q Consensus 233 AI~lYlLLD~~~~~p~~~~~~lle~Fa~tF~Ip~~~~~~iqgfWlLDdh~d~aleeA~~LLP~is~-P~~h~kIlqvLl~ 311 (801)
+||||||+|++++.+ ++++++||++|+||++++++|+|||+|| |+++ ++||++|+.++. ||+|++|+++|++
T Consensus 48 ~l~~YlLlD~~~~~~----~~~~~~Fa~~f~ip~~~~~~~~g~W~LD-~~~~--~~A~~~L~~ps~~~~~~~~Il~~L~~ 120 (226)
T PF13934_consen 48 SLFYYLLLDLDDTRP----SELAESFARAFGIPPKYIKFIQGFWLLD-HGDF--EEALELLSHPSLIPWFPDKILQALLR 120 (226)
T ss_pred HHHHHHHHhcCcccc----ccHHHHHHHHhCCCHHHHHHHHHHHHhC-hHhH--HHHHHHhCCCCCCcccHHHHHHHHHH
Confidence 999999999999866 3678999999999999999999999999 9998 999999988766 8999999999999
Q ss_pred CCCchhhHHHHhhccCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHHhhchHHHhhhhccCCcCccccccccCccchH
Q 003705 312 RENPEAALMVLRWSGRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQRMLCTKVREKKLKFGTIGETFDDLQGGFKTWE 391 (801)
Q Consensus 312 ~g~~~~AL~ylr~~g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~~~~~~~e~~~~~~~~~~~~~~~~~~~~~w~ 391 (801)
+|+++.||+|+|+++ |++.+. ++++.++++|+|++|+|||+|+|+++++.+.+
T Consensus 121 ~~~~~lAL~y~~~~~----p~l~s~-~~~~~~~~~La~~~v~EAf~~~R~~~~~~~~~---------------------- 173 (226)
T PF13934_consen 121 RGDPKLALRYLRAVG----PPLSSP-EALTLYFVALANGLVTEAFSFQRSYPDELRRR---------------------- 173 (226)
T ss_pred CCChhHHHHHHHhcC----CCCCCH-HHHHHHHHHHHcCCHHHHHHHHHhCchhhhHH----------------------
Confidence 999999999999996 656655 77888888899999999999999999976531
Q ss_pred HHHHHHHHHHHHhhhhcchHHHhhcCCCChhhHHHHHHHhccCCCCCCCCCcchHHHH
Q 003705 392 QWLEVLVTEICCLCIRRNLVDRMIELPWNTDEEKYLHKCLLDSATDDPSTTVGSLLVV 449 (801)
Q Consensus 392 ~~~E~Ll~~~f~~C~~~~~l~~LL~LPLd~eEEe~L~k~L~~~~~~~p~~~~~sLLlV 449 (801)
.++.|++++++.|.+.+++++|++|||+++||+||++||+++++.. ++++++|
T Consensus 174 -l~e~l~~~~~~~~~~~~~~~~Ll~LPl~~~EE~~l~~~L~~~~~~~----~~~~ll~ 226 (226)
T PF13934_consen 174 -LFEQLLEHCLEECARSGRLDELLSLPLDEEEEQWLEKYLRESPGRQ----AQDLLLM 226 (226)
T ss_pred -HHHHHHHHHHHHhhhhhHHHHHHhCCCChHHHHHHHHHHccCCCcc----ccCeeeC
Confidence 3688999999998889999999999999999999999999999887 4777664
No 2
>PLN03077 Protein ECB2; Provisional
Probab=76.71 E-value=66 Score=39.68 Aligned_cols=126 Identities=14% Similarity=0.060 Sum_probs=75.4
Q ss_pred hHHHHHHHHcCCCchhhHHHHhhccCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHHhhchHHHhhhhccCCcCcccc
Q 003705 302 HPKIAQVLLERENPEAALMVLRWSGRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQRMLCTKVREKKLKFGTIGETFD 381 (801)
Q Consensus 302 h~kIlqvLl~~g~~~~AL~ylr~~g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~~~~~~~e~~~~~~~~~~~~~ 381 (801)
...+|..+...|+.+.|..++..+. .|.+.+. -..+.....+|.+.||+.+-+.-... . -..+
T Consensus 326 ~n~Li~~y~k~g~~~~A~~vf~~m~---~~d~~s~---n~li~~~~~~g~~~~A~~lf~~M~~~--g------~~Pd--- 388 (857)
T PLN03077 326 CNSLIQMYLSLGSWGEAEKVFSRME---TKDAVSW---TAMISGYEKNGLPDKALETYALMEQD--N------VSPD--- 388 (857)
T ss_pred HHHHHHHHHhcCCHHHHHHHHhhCC---CCCeeeH---HHHHHHHHhCCCHHHHHHHHHHHHHh--C------CCCC---
Confidence 3447777788899999999888875 2444443 35677788889999998877653221 0 0001
Q ss_pred ccccCccchHHHHHHHHHHHHHhhhhcchHHHhhcCCCChhhHHHHHHHhccCCCCCCCCCcchHHHHHHHhhcChhHHH
Q 003705 382 DLQGGFKTWEQWLEVLVTEICCLCIRRNLVDRMIELPWNTDEEKYLHKCLLDSATDDPSTTVGSLLVVFYIQRYRYAEAY 461 (801)
Q Consensus 382 ~~~~~~~~w~~~~E~Ll~~~f~~C~~~~~l~~LL~LPLd~eEEe~L~k~L~~~~~~~p~~~~~sLLlVyyLQR~RYiEAv 461 (801)
..-+..++..|...+.+++- ..++++..+. +..+.....+.|+-.|.+.|++.+|.
T Consensus 389 -------------~~t~~~ll~a~~~~g~~~~a----------~~l~~~~~~~-g~~~~~~~~n~Li~~y~k~g~~~~A~ 444 (857)
T PLN03077 389 -------------EITIASVLSACACLGDLDVG----------VKLHELAERK-GLISYVVVANALIEMYSKCKCIDKAL 444 (857)
T ss_pred -------------ceeHHHHHHHHhccchHHHH----------HHHHHHHHHh-CCCcchHHHHHHHHHHHHcCCHHHHH
Confidence 12233344455555554433 2233334332 22233344566777788888888888
Q ss_pred HHHHHhh
Q 003705 462 QVNLKLQ 468 (801)
Q Consensus 462 qv~~kL~ 468 (801)
++..++.
T Consensus 445 ~vf~~m~ 451 (857)
T PLN03077 445 EVFHNIP 451 (857)
T ss_pred HHHHhCC
Confidence 8888775
No 3
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=76.62 E-value=1.3e+02 Score=36.36 Aligned_cols=25 Identities=12% Similarity=0.030 Sum_probs=18.3
Q ss_pred chHHHHHHHhhcChhHHHHHHHHhh
Q 003705 444 GSLLVVFYIQRYRYAEAYQVNLKLQ 468 (801)
Q Consensus 444 ~sLLlVyyLQR~RYiEAvqv~~kL~ 468 (801)
-+.++--|.+.|++.||+++.++++
T Consensus 293 ~n~li~~y~~~g~~~eA~~lf~~M~ 317 (697)
T PLN03081 293 WNSMLAGYALHGYSEEALCLYYEMR 317 (697)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4566677777888888888877774
No 4
>PLN03077 Protein ECB2; Provisional
Probab=66.94 E-value=1.8e+02 Score=35.90 Aligned_cols=124 Identities=14% Similarity=0.083 Sum_probs=79.4
Q ss_pred hHHHHHHHHcCCCchhhHHHHhhccCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHHhhchHHHhhhhccCCcCcccc
Q 003705 302 HPKIAQVLLERENPEAALMVLRWSGRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQRMLCTKVREKKLKFGTIGETFD 381 (801)
Q Consensus 302 h~kIlqvLl~~g~~~~AL~ylr~~g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~~~~~~~e~~~~~~~~~~~~~ 381 (801)
...+|..+...|+.+.|+.++..+.. +.+.+. -..+..+..+|...||+.+-+.....++ + +
T Consensus 427 ~n~Li~~y~k~g~~~~A~~vf~~m~~---~d~vs~---~~mi~~~~~~g~~~eA~~lf~~m~~~~~----p-----d--- 488 (857)
T PLN03077 427 ANALIEMYSKCKCIDKALEVFHNIPE---KDVISW---TSIIAGLRLNNRCFEALIFFRQMLLTLK----P-----N--- 488 (857)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHhCCC---CCeeeH---HHHHHHHHHCCCHHHHHHHHHHHHhCCC----C-----C---
Confidence 44578888899999999999998852 444444 3567778899999999998877532211 0 1
Q ss_pred ccccCccchHHHHHHHHHHHHHhhhhcchHHHhhcCCCChhhHHHHHHHhccCCCCCCCCCcchHHHHHHHhhcChhHHH
Q 003705 382 DLQGGFKTWEQWLEVLVTEICCLCIRRNLVDRMIELPWNTDEEKYLHKCLLDSATDDPSTTVGSLLVVFYIQRYRYAEAY 461 (801)
Q Consensus 382 ~~~~~~~~w~~~~E~Ll~~~f~~C~~~~~l~~LL~LPLd~eEEe~L~k~L~~~~~~~p~~~~~sLLlVyyLQR~RYiEAv 461 (801)
..-+..++..|.+.+.++ +-+.++.+..... ..+.....+.|+-.|.+.|++.+|.
T Consensus 489 -------------~~t~~~lL~a~~~~g~l~----------~~~~i~~~~~~~g-~~~~~~~~naLi~~y~k~G~~~~A~ 544 (857)
T PLN03077 489 -------------SVTLIAALSACARIGALM----------CGKEIHAHVLRTG-IGFDGFLPNALLDLYVRCGRMNYAW 544 (857)
T ss_pred -------------HhHHHHHHHHHhhhchHH----------HhHHHHHHHHHhC-CCccceechHHHHHHHHcCCHHHHH
Confidence 234445566666555543 3455555554433 2233334566777777888888887
Q ss_pred HHHHHh
Q 003705 462 QVNLKL 467 (801)
Q Consensus 462 qv~~kL 467 (801)
++....
T Consensus 545 ~~f~~~ 550 (857)
T PLN03077 545 NQFNSH 550 (857)
T ss_pred HHHHhc
Confidence 766544
No 5
>PF10366 Vps39_1: Vacuolar sorting protein 39 domain 1; InterPro: IPR019452 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised.
Probab=66.90 E-value=26 Score=33.13 Aligned_cols=88 Identities=19% Similarity=0.177 Sum_probs=59.4
Q ss_pred hcchHHHhhcCCCChhhHHHHHHHhccCCCCCCCCCcchHHHHHHHhhcChhHHHHHHHHhhhhhhh-cccCCCccHHHH
Q 003705 407 RRNLVDRMIELPWNTDEEKYLHKCLLDSATDDPSTTVGSLLVVFYIQRYRYAEAYQVNLKLQSVEQD-FISKNPVSEEVL 485 (801)
Q Consensus 407 ~~~~l~~LL~LPLd~eEEe~L~k~L~~~~~~~p~~~~~sLLlVyyLQR~RYiEAvqv~~kL~s~eq~-~~~~~s~see~~ 485 (801)
+...+..++..| |.=.-+..+++|.+.+.- .-|+.||-+||.+.+|+++..++..-+.. ... +..
T Consensus 13 ~~~~l~~llr~~-N~C~~~~~e~~L~~~~~~-------~eL~~lY~~kg~h~~AL~ll~~l~~~~~~~~~~------~~~ 78 (108)
T PF10366_consen 13 NPSLLGPLLRLP-NYCDLEEVEEVLKEHGKY-------QELVDLYQGKGLHRKALELLKKLADEEDSDEED------PFL 78 (108)
T ss_pred CHHHHHHHHccC-CcCCHHHHHHHHHHcCCH-------HHHHHHHHccCccHHHHHHHHHHhccccccccc------ccc
Confidence 557788888888 777777778889776543 36788888999999999999999621000 000 000
Q ss_pred HHhHhhHHHHHHHHHHHhhhchHHHHHHHH
Q 003705 486 SRMQSQIHWRTKFIDTSIELLPEVQRQLLK 515 (801)
Q Consensus 486 ~r~r~~s~~R~~Lv~~y~~~LP~VQR~l~~ 515 (801)
+.. ..+|-+|.+-||.-+..++-
T Consensus 79 ~~~-------~~~iv~yL~~L~~~~~dLI~ 101 (108)
T PF10366_consen 79 SGV-------KETIVQYLQKLGNEDLDLIF 101 (108)
T ss_pred cCc-------hhHHHHHHHhCChhhhHHHH
Confidence 000 13356899999887776653
No 6
>KOG2377 consensus Uncharacterized conserved protein [Function unknown]
Probab=64.84 E-value=4.4 Score=47.24 Aligned_cols=50 Identities=32% Similarity=0.343 Sum_probs=38.8
Q ss_pred HhhhccCCCcH---HHHHHhhhCCCCCCCCChHHHHHHHHcCCCchhhHHHHhh-ccC
Q 003705 274 TFYLLDDQADE---ALQEACHLLPEISGPTTHPKIAQVLLERENPEAALMVLRW-SGR 327 (801)
Q Consensus 274 gfWlLDdh~d~---aleeA~~LLP~is~P~~h~kIlqvLl~~g~~~~AL~ylr~-~g~ 327 (801)
+|.+|| |+.+ .-+-++++|-.++ .|+.||++|+.+|++=.||+|++. .|+
T Consensus 547 Ac~LLs-~~~~~~~~~ql~lDML~rls---aH~~iIevll~~G~vl~ALR~A~~~~g~ 600 (657)
T KOG2377|consen 547 ACLLLS-LESFYPPAHQLSLDMLKRLS---AHDEIIEVLLSKGQVLAALRFARGIGGH 600 (657)
T ss_pred eEEEec-ccCcCccHHHHhHHHHhhhh---hhHHHHHHHHcCchHHHHHHHHhhccCc
Confidence 567787 7644 4567777776554 499999999999999999999994 443
No 7
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=63.35 E-value=1.1e+02 Score=36.81 Aligned_cols=56 Identities=11% Similarity=-0.048 Sum_probs=34.0
Q ss_pred ChHHHHHHHHcCCCchhhHHHHhhccCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHHhh
Q 003705 301 THPKIAQVLLERENPEAALMVLRWSGRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQRML 362 (801)
Q Consensus 301 ~h~kIlqvLl~~g~~~~AL~ylr~~g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~~ 362 (801)
....+|..+...|+.+.|..++..+.. +.+.+. -..+.....+|.+.||+.+-+..
T Consensus 261 ~~n~Li~~y~k~g~~~~A~~vf~~m~~---~~~vt~---n~li~~y~~~g~~~eA~~lf~~M 316 (697)
T PLN03081 261 VSCALIDMYSKCGDIEDARCVFDGMPE---KTTVAW---NSMLAGYALHGYSEEALCLYYEM 316 (697)
T ss_pred eHHHHHHHHHHCCCHHHHHHHHHhCCC---CChhHH---HHHHHHHHhCCCHHHHHHHHHHH
Confidence 344566777777777777777776641 222222 24556667777777777666543
No 8
>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Probab=62.61 E-value=14 Score=37.73 Aligned_cols=39 Identities=28% Similarity=0.242 Sum_probs=31.5
Q ss_pred HHHHHhhhCCCCCCCCChHHHHHHHHcCCCchhhHHHHhhc
Q 003705 285 ALQEACHLLPEISGPTTHPKIAQVLLERENPEAALMVLRWS 325 (801)
Q Consensus 285 aleeA~~LLP~is~P~~h~kIlqvLl~~g~~~~AL~ylr~~ 325 (801)
..+-|+++|=.. ..-|..|+++|+..|++-.||+|++..
T Consensus 77 ~~Ql~lDMLkRL--~~~~~~iievLL~~g~vl~ALr~ar~~ 115 (167)
T PF07035_consen 77 AYQLGLDMLKRL--GTAYEEIIEVLLSKGQVLEALRYARQY 115 (167)
T ss_pred HHHHHHHHHHHh--hhhHHHHHHHHHhCCCHHHHHHHHHHc
Confidence 457888887333 234889999999999999999999985
No 9
>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.
Probab=61.89 E-value=14 Score=42.82 Aligned_cols=83 Identities=22% Similarity=0.245 Sum_probs=54.7
Q ss_pred hCCChhhHHHHhHhhhccCCCcHHHHH------HhhhCCCCCCCCChHHHHHHHHcCCCchhhHHHHhhccCCCCCCccC
Q 003705 262 FSITRHSLLESLTFYLLDDQADEALQE------ACHLLPEISGPTTHPKIAQVLLERENPEAALMVLRWSGRDGGSLLVS 335 (801)
Q Consensus 262 F~Ip~~~~~~iqgfWlLDdh~d~alee------A~~LLP~is~P~~h~kIlqvLl~~g~~~~AL~ylr~~g~~~~P~l~s 335 (801)
+.|+...+.+-.+.. +.|+ +. +=.++|.+. +.++.+|+.-|-.+|.++.||.+.+-.
T Consensus 259 ~~ld~~~~~fk~av~----~~d~--~~v~~~i~~~~ll~~i~-~~~~~~i~~fL~~~G~~e~AL~~~~D~---------- 321 (443)
T PF04053_consen 259 YELDLSELEFKTAVL----RGDF--EEVLRMIAASNLLPNIP-KDQGQSIARFLEKKGYPELALQFVTDP---------- 321 (443)
T ss_dssp EE--HHHHHHHHHHH----TT-H--HH-----HHHHTGGG---HHHHHHHHHHHHHTT-HHHHHHHSS-H----------
T ss_pred EEECHHHHHHHHHHH----cCCh--hhhhhhhhhhhhcccCC-hhHHHHHHHHHHHCCCHHHHHhhcCCh----------
Confidence 445555555555444 3444 45 245556664 466888999999999999999976432
Q ss_pred hHHHHHHHHHHHhcCChhHHHHHHHhhchH
Q 003705 336 LSEAVTAVRIRVECALLTEAFTYQRMLCTK 365 (801)
Q Consensus 336 lsEA~l~l~VlLan~lItEAF~~~R~~~~~ 365 (801)
.....+.|++|.+.+|+..++...+.
T Consensus 322 ----~~rFeLAl~lg~L~~A~~~a~~~~~~ 347 (443)
T PF04053_consen 322 ----DHRFELALQLGNLDIALEIAKELDDP 347 (443)
T ss_dssp ----HHHHHHHHHCT-HHHHHHHCCCCSTH
T ss_pred ----HHHhHHHHhcCCHHHHHHHHHhcCcH
Confidence 36888999999999999999876543
No 10
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.49 E-value=34 Score=42.43 Aligned_cols=161 Identities=17% Similarity=0.115 Sum_probs=88.7
Q ss_pred hhccCCCcHHHHHHhhhCCCCCC--C-CChH----HHHHHHHcCCCchhhHHHHhhccCCCCCCccChHHHHHHHHHHHh
Q 003705 276 YLLDDQADEALQEACHLLPEISG--P-TTHP----KIAQVLLERENPEAALMVLRWSGRDGGSLLVSLSEAVTAVRIRVE 348 (801)
Q Consensus 276 WlLDdh~d~aleeA~~LLP~is~--P-~~h~----kIlqvLl~~g~~~~AL~ylr~~g~~~~P~l~slsEA~l~l~VlLa 348 (801)
|+|- |..| ++|+...-.... | .... .+|.-|+..|+++.|=+...-+-+ ..+.+.+..++++.+
T Consensus 365 Wll~-~k~y--eeAl~~~k~~~~~~~~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~g------n~~~eWe~~V~~f~e 435 (846)
T KOG2066|consen 365 WLLE-KKKY--EEALDAAKASIGNEERFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLG------NNAAEWELWVFKFAE 435 (846)
T ss_pred HHHH-hhHH--HHHHHHHHhccCCccccchHHHHHHHHHHHHhcchHHHHHhhhHHHhc------chHHHHHHHHHHhcc
Confidence 6666 7777 777765411111 1 1222 266677778888777665544421 136677777888888
Q ss_pred cCChhHHHHHHHhhchHHHhhhhccCCcCccccccccCccchHHHHHHHHHHHHHhhhhcchHHHhhcCCCChhhHHHHH
Q 003705 349 CALLTEAFTYQRMLCTKVREKKLKFGTIGETFDDLQGGFKTWEQWLEVLVTEICCLCIRRNLVDRMIELPWNTDEEKYLH 428 (801)
Q Consensus 349 n~lItEAF~~~R~~~~~~~e~~~~~~~~~~~~~~~~~~~~~w~~~~E~Ll~~~f~~C~~~~~l~~LL~LPLd~eEEe~L~ 428 (801)
++++++=+-|.-..+.+++- ...+.+|.+++. -...+-++-+=+-|-+-.--.++.
T Consensus 436 ~~~l~~Ia~~lPt~~~rL~p-----------------------~vYemvLve~L~-~~~~~F~e~i~~Wp~~Lys~l~ii 491 (846)
T KOG2066|consen 436 LDQLTDIAPYLPTGPPRLKP-----------------------LVYEMVLVEFLA-SDVKGFLELIKEWPGHLYSVLTII 491 (846)
T ss_pred ccccchhhccCCCCCcccCc-----------------------hHHHHHHHHHHH-HHHHHHHHHHHhCChhhhhhhHHH
Confidence 88777777766554433221 123444444443 333344444444444433333333
Q ss_pred HHhccCC-CCCCCCCcchHHHHHHHhhcChhHHHHHHHHhhh
Q 003705 429 KCLLDSA-TDDPSTTVGSLLVVFYIQRYRYAEAYQVNLKLQS 469 (801)
Q Consensus 429 k~L~~~~-~~~p~~~~~sLLlVyyLQR~RYiEAvqv~~kL~s 469 (801)
+-....- ...-.++..++|.-.|+-.+.|..|.+.+-+++.
T Consensus 492 sa~~~q~~q~Se~~~L~e~La~LYl~d~~Y~~Al~~ylklk~ 533 (846)
T KOG2066|consen 492 SATEPQIKQNSESTALLEVLAHLYLYDNKYEKALPIYLKLQD 533 (846)
T ss_pred hhcchHHHhhccchhHHHHHHHHHHHccChHHHHHHHHhccC
Confidence 3221110 1111123456788889999999999999999974
No 11
>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm
Probab=58.03 E-value=1.4e+02 Score=33.37 Aligned_cols=94 Identities=12% Similarity=0.041 Sum_probs=67.2
Q ss_pred HHHHHHhHhCCChhhHHHHhHhhhccCCCcHHHHHHhhhCCC-CCCCCChHHHHHHHHcCCCchhhHHHHhhccCCCCCC
Q 003705 254 IVDDFAATFSITRHSLLESLTFYLLDDQADEALQEACHLLPE-ISGPTTHPKIAQVLLERENPEAALMVLRWSGRDGGSL 332 (801)
Q Consensus 254 lle~Fa~tF~Ip~~~~~~iqgfWlLDdh~d~aleeA~~LLP~-is~P~~h~kIlqvLl~~g~~~~AL~ylr~~g~~~~P~ 332 (801)
.+++....|.||.+-.-.+..--+.+ ..++ + .++-+.. -..|==..-++.+++..|+++.|..|+.-. +
T Consensus 195 ~A~kl~k~Fkv~dkrfw~lki~aLa~-~~~w--~-eL~~fa~skKsPIGyepFv~~~~~~~~~~eA~~yI~k~-----~- 264 (319)
T PF04840_consen 195 QAEKLKKEFKVPDKRFWWLKIKALAE-NKDW--D-ELEKFAKSKKSPIGYEPFVEACLKYGNKKEASKYIPKI-----P- 264 (319)
T ss_pred HHHHHHHHcCCcHHHHHHHHHHHHHh-cCCH--H-HHHHHHhCCCCCCChHHHHHHHHHCCCHHHHHHHHHhC-----C-
Confidence 47889999999998776666666676 6776 2 2222211 223533444899999999999999999764 2
Q ss_pred ccChHHHHHHHHHHHhcCChhHHHHHHHhhc
Q 003705 333 LVSLSEAVTAVRIRVECALLTEAFTYQRMLC 363 (801)
Q Consensus 333 l~slsEA~l~l~VlLan~lItEAF~~~R~~~ 363 (801)
. ...+...+.||...||-..+.+.-
T Consensus 265 ---~---~~rv~~y~~~~~~~~A~~~A~~~k 289 (319)
T PF04840_consen 265 ---D---EERVEMYLKCGDYKEAAQEAFKEK 289 (319)
T ss_pred ---h---HHHHHHHHHCCCHHHHHHHHHHcC
Confidence 1 256777899999999999886653
No 12
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=54.70 E-value=2.7e+02 Score=30.10 Aligned_cols=86 Identities=13% Similarity=0.080 Sum_probs=46.4
Q ss_pred HHhHhhhccCCCcHHHHHHhhhCCC-CCCCC--------ChHHHHHHHHcCCCchhhHHHHhhccCCCCCCccChHHHHH
Q 003705 271 ESLTFYLLDDQADEALQEACHLLPE-ISGPT--------THPKIAQVLLERENPEAALMVLRWSGRDGGSLLVSLSEAVT 341 (801)
Q Consensus 271 ~iqgfWlLDdh~d~aleeA~~LLP~-is~P~--------~h~kIlqvLl~~g~~~~AL~ylr~~g~~~~P~l~slsEA~l 341 (801)
...|..++. .+++ ++|+.++-. +..|. ....+...++..|+++.|+.++...-.. .|. ...-...
T Consensus 73 ~~la~~~~~-~g~~--~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~-~~~--~~~~~~~ 146 (389)
T PRK11788 73 LALGNLFRR-RGEV--DRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAEELFLQLVDE-GDF--AEGALQQ 146 (389)
T ss_pred HHHHHHHHH-cCcH--HHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHcC-Ccc--hHHHHHH
Confidence 344555555 6666 666655421 11221 1223466677889999998877665311 121 1111223
Q ss_pred HHHHHHhcCChhHHHHHHHhh
Q 003705 342 AVRIRVECALLTEAFTYQRML 362 (801)
Q Consensus 342 ~l~VlLan~lItEAF~~~R~~ 362 (801)
...+....|...+|....+..
T Consensus 147 la~~~~~~g~~~~A~~~~~~~ 167 (389)
T PRK11788 147 LLEIYQQEKDWQKAIDVAERL 167 (389)
T ss_pred HHHHHHHhchHHHHHHHHHHH
Confidence 445666777888887766654
No 13
>PLN03218 maturation of RBCL 1; Provisional
Probab=51.93 E-value=2.5e+02 Score=36.52 Aligned_cols=54 Identities=11% Similarity=0.129 Sum_probs=30.6
Q ss_pred hHHHHHHHHcCCCchhhHHHHhhccCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHHh
Q 003705 302 HPKIAQVLLERENPEAALMVLRWSGRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQRM 361 (801)
Q Consensus 302 h~kIlqvLl~~g~~~~AL~ylr~~g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~ 361 (801)
+..|+..+...|..+.|+.+++.+.. |...+. -..+.+...+|.+.+|+.+.+.
T Consensus 409 ~~~li~~~~~~g~~~eAl~lf~~M~~---pd~~Ty---n~LL~a~~k~g~~e~A~~lf~~ 462 (1060)
T PLN03218 409 HAKFFKACKKQRAVKEAFRFAKLIRN---PTLSTF---NMLMSVCASSQDIDGALRVLRL 462 (1060)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCC---CCHHHH---HHHHHHHHhCcCHHHHHHHHHH
Confidence 34455566667777777777666641 322222 2345555666677777666544
No 14
>PLN03218 maturation of RBCL 1; Provisional
Probab=50.46 E-value=1.9e+02 Score=37.52 Aligned_cols=56 Identities=9% Similarity=0.057 Sum_probs=29.1
Q ss_pred HHHHHHHHcCCCchhhHHHHhhccCCC-CCCccChHHHHHHHHHHHhcCChhHHHHHHHh
Q 003705 303 PKIAQVLLERENPEAALMVLRWSGRDG-GSLLVSLSEAVTAVRIRVECALLTEAFTYQRM 361 (801)
Q Consensus 303 ~kIlqvLl~~g~~~~AL~ylr~~g~~~-~P~l~slsEA~l~l~VlLan~lItEAF~~~R~ 361 (801)
..+|..+...|+.+.|+.++.-+...| .|...+. -..+.....+|.+-+|+.+.+.
T Consensus 476 nsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTy---naLI~gy~k~G~~eeAl~lf~~ 532 (1060)
T PLN03218 476 TTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTF---GALIDGCARAGQVAKAFGAYGI 532 (1060)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHH---HHHHHHHHHCcCHHHHHHHHHH
Confidence 345566666666666666665553222 1222211 2345556666666666665443
No 15
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=48.79 E-value=3e+02 Score=33.98 Aligned_cols=175 Identities=12% Similarity=0.054 Sum_probs=92.4
Q ss_pred hHHHHHHhHhCCC---hhhHHHHhHhhhccCCCcHHHHHHhhhCCCC-C-CC-------CChHHHHHHHHcCCCchhhHH
Q 003705 253 HIVDDFAATFSIT---RHSLLESLTFYLLDDQADEALQEACHLLPEI-S-GP-------TTHPKIAQVLLERENPEAALM 320 (801)
Q Consensus 253 ~lle~Fa~tF~Ip---~~~~~~iqgfWlLDdh~d~aleeA~~LLP~i-s-~P-------~~h~kIlqvLl~~g~~~~AL~ 320 (801)
..+..|...-... +.+.....+--++. -+++ ++|..++-.+ . .| .....+..+++.+|+++.|+.
T Consensus 255 eA~~~~~~ll~~~~~~P~~a~~~la~~yl~-~g~~--e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~ 331 (765)
T PRK10049 255 DVISEYQRLKAEGQIIPPWAQRWVASAYLK-LHQP--EKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALT 331 (765)
T ss_pred HHHHHHHHhhccCCCCCHHHHHHHHHHHHh-cCCc--HHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHH
Confidence 4455666655553 44444444555665 5555 5555543111 0 11 123345667789999999998
Q ss_pred HHhhccCCCCCCc--------cChH----HH-HHHHHHHHhcCChhHHHHHHHhhchHHHhhhhccCCcCccccccccCc
Q 003705 321 VLRWSGRDGGSLL--------VSLS----EA-VTAVRIRVECALLTEAFTYQRMLCTKVREKKLKFGTIGETFDDLQGGF 387 (801)
Q Consensus 321 ylr~~g~~~~P~l--------~sls----EA-~l~l~VlLan~lItEAF~~~R~~~~~~~e~~~~~~~~~~~~~~~~~~~ 387 (801)
++...... .|+- ..+. ++ .+...+++..|...||....+........ +
T Consensus 332 ~l~~~~~~-~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~---------n--------- 392 (765)
T PRK10049 332 VTAHTINN-SPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPG---------N--------- 392 (765)
T ss_pred HHHHHhhc-CCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC---------C---------
Confidence 87754321 1210 0001 12 34556777888888888877665332110 0
Q ss_pred cchHHHHHHHHHHHHHhhhhcchHHHhhcCCCChhhHHHHHHHhccCCCCCCCCCcchHHHHHHHhhcChhHHHHHHHHh
Q 003705 388 KTWEQWLEVLVTEICCLCIRRNLVDRMIELPWNTDEEKYLHKCLLDSATDDPSTTVGSLLVVFYIQRYRYAEAYQVNLKL 467 (801)
Q Consensus 388 ~~w~~~~E~Ll~~~f~~C~~~~~l~~LL~LPLd~eEEe~L~k~L~~~~~~~p~~~~~sLLlVyyLQR~RYiEAvqv~~kL 467 (801)
..|... +...+...=..++-+++|.+-|...+.. + ...-.+.+-+++.++|.+|.++.+++
T Consensus 393 -------~~l~~~---------lA~l~~~~g~~~~A~~~l~~al~l~Pd~-~--~l~~~~a~~al~~~~~~~A~~~~~~l 453 (765)
T PRK10049 393 -------QGLRID---------YASVLQARGWPRAAENELKKAEVLEPRN-I--NLEVEQAWTALDLQEWRQMDVLTDDV 453 (765)
T ss_pred -------HHHHHH---------HHHHHHhcCCHHHHHHHHHHHHhhCCCC-h--HHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 111111 1122223333355566777766543211 1 01224445688999999999999998
Q ss_pred h
Q 003705 468 Q 468 (801)
Q Consensus 468 ~ 468 (801)
.
T Consensus 454 l 454 (765)
T PRK10049 454 V 454 (765)
T ss_pred H
Confidence 5
No 16
>PF05405 Mt_ATP-synt_B: Mitochondrial ATP synthase B chain precursor (ATP-synt_B); InterPro: IPR008688 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit B from the F0 complex in F-ATPases found in mitochondria of eukaryotes (metazoa, viridiplantae (plants and green algae), jakobidae and the malawimonadidae). The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); PDB: 2WSS_X 2CLY_D.
Probab=48.67 E-value=2e+02 Score=28.57 Aligned_cols=55 Identities=18% Similarity=0.253 Sum_probs=37.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHhhHHHHHHHHh
Q 003705 18 EVVVKDWCKRAFKNIIAELKLIYNLEVEVMKTRLSLLLKFQMKLRDISSVIEVLA 72 (801)
Q Consensus 18 ~~vV~dW~~~~~~~~~sel~~I~~~~~~~~~~~l~~L~~~~~qL~~Ls~Vl~~L~ 72 (801)
|..|++|.-.....+..+++...+......+.++..-.+..-....+..++++.-
T Consensus 35 g~~i~~~ld~~~~~i~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~~k 89 (163)
T PF05405_consen 35 GPSIAEWLDERIQKIEDELNQSRNDHIKALKERIEQVKKEQSLVEGTKMLFEASK 89 (163)
T ss_dssp -----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 6789999999999999999999988888888887765544444555555555444
No 17
>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]
Probab=40.80 E-value=3.2e+02 Score=35.91 Aligned_cols=218 Identities=19% Similarity=0.181 Sum_probs=111.5
Q ss_pred HHhHhCCChhhHHHHhHhhhccCCCcHHHHHHhhhC-------CC----CCCCCChHHHH----HHHHcCCCchhhH-HH
Q 003705 258 FAATFSITRHSLLESLTFYLLDDQADEALQEACHLL-------PE----ISGPTTHPKIA----QVLLERENPEAAL-MV 321 (801)
Q Consensus 258 Fa~tF~Ip~~~~~~iqgfWlLDdh~d~aleeA~~LL-------P~----is~P~~h~kIl----qvLl~~g~~~~AL-~y 321 (801)
--+.|.|...+-....++.||=.-+.....++..+. ++ ..++.+...|. .-|.+.+.++.|. +|
T Consensus 883 ~~rkF~ID~~L~ry~~AL~hLs~~~~~~~~e~~n~I~kh~Ly~~aL~ly~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Y 962 (1265)
T KOG1920|consen 883 LLRKFKIDDYLKRYEDALSHLSECGETYFPECKNYIKKHGLYDEALALYKPDSEKQKVIYEAYADHLREELMSDEAALMY 962 (1265)
T ss_pred hhhheeHHHHHHHHHHHHHHHHHcCccccHHHHHHHHhcccchhhhheeccCHHHHHHHHHHHHHHHHHhccccHHHHHH
Confidence 346778887777788888877421211123333332 00 11112222232 3455677776665 55
Q ss_pred HhhccCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHHhhchHHHhhhhccCCcCccccccccCccchHHHHHHHHHHH
Q 003705 322 LRWSGRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQRMLCTKVREKKLKFGTIGETFDDLQGGFKTWEQWLEVLVTEI 401 (801)
Q Consensus 322 lr~~g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~~~~~~~e~~~~~~~~~~~~~~~~~~~~~w~~~~E~Ll~~~ 401 (801)
.++ | .+++ ++.-...||...||...+++...... .+-.|-..+
T Consensus 963 e~~-G--------klek---Al~a~~~~~dWr~~l~~a~ql~~~~d-------------------------e~~~~a~~L 1005 (1265)
T KOG1920|consen 963 ERC-G--------KLEK---ALKAYKECGDWREALSLAAQLSEGKD-------------------------ELVILAEEL 1005 (1265)
T ss_pred HHh-c--------cHHH---HHHHHHHhccHHHHHHHHHhhcCCHH-------------------------HHHHHHHHH
Confidence 544 3 2555 45557789999999999887543211 012222444
Q ss_pred HHhhhhcchHHHhhcCCCChhhHHHHHHHhccCCCCCCCCCcchHHHHHHHhhcChhHHHHHHHHhhhhhhhcccCCCcc
Q 003705 402 CCLCIRRNLVDRMIELPWNTDEEKYLHKCLLDSATDDPSTTVGSLLVVFYIQRYRYAEAYQVNLKLQSVEQDFISKNPVS 481 (801)
Q Consensus 402 f~~C~~~~~l~~LL~LPLd~eEEe~L~k~L~~~~~~~p~~~~~sLLlVyyLQR~RYiEAvqv~~kL~s~eq~~~~~~s~s 481 (801)
+..|.+.++-.+. -+.+.+||.+..+ .+.-|+.-.+|.||..+...-+ +-+.++
T Consensus 1006 ~s~L~e~~kh~eA---------a~il~e~~sd~~~----------av~ll~ka~~~~eAlrva~~~~--~~d~ie----- 1059 (1265)
T KOG1920|consen 1006 VSRLVEQRKHYEA---------AKILLEYLSDPEE----------AVALLCKAKEWEEALRVASKAK--RDDIIE----- 1059 (1265)
T ss_pred HHHHHHcccchhH---------HHHHHHHhcCHHH----------HHHHHhhHhHHHHHHHHHHhcc--cchHHH-----
Confidence 4444444333222 2456667755432 2667888889999998888664 112222
Q ss_pred HHHHHHhHhhHHHHHHHHHHHhh-hchHHHHHHHHhCCCCcccccc-cccccccCCCCC
Q 003705 482 EEVLSRMQSQIHWRTKFIDTSIE-LLPEVQRQLLKNGKLPLNALNS-SEEVEIPEKSDL 538 (801)
Q Consensus 482 ee~~~r~r~~s~~R~~Lv~~y~~-~LP~VQR~l~~~~~~~~~~~~~-~~~~~~~~~~~~ 538 (801)
+-..+-+.++...-...++...+ ..-.-+|=++.+.|+......+ .++|+-.+..|+
T Consensus 1060 e~l~~al~e~~~~~~~~L~~~k~~f~~yk~RLl~vRe~k~~~~~~~~~~ev~~d~d~dl 1118 (1265)
T KOG1920|consen 1060 EVLKPALLEAFGEVLEFLEDVKEQFVKYKKRLLVVRENKEKRPEAFADGEVEHDLDDDL 1118 (1265)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhchhhhhccccCccccccc
Confidence 23344445444433344444222 2233344445554444333344 777776444444
No 18
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=38.32 E-value=5.2e+02 Score=30.35 Aligned_cols=42 Identities=10% Similarity=-0.058 Sum_probs=26.0
Q ss_pred HHHHHHHhccCCCCCCCCCcchHHHHHHHhhcChhHHHHHHHHhh
Q 003705 424 EKYLHKCLLDSATDDPSTTVGSLLVVFYIQRYRYAEAYQVNLKLQ 468 (801)
Q Consensus 424 Ee~L~k~L~~~~~~~p~~~~~sLLlVyyLQR~RYiEAvqv~~kL~ 468 (801)
.+++.+.+...+.. .....++-..|.+.|+|.+|.+..++.-
T Consensus 179 ~~~~~~~~~~~~~~---~~~~~~~~~~~~~~g~~~~A~~~~~~a~ 220 (899)
T TIGR02917 179 RALIDEVLTADPGN---VDALLLKGDLLLSLGNIELALAAYRKAI 220 (899)
T ss_pred HHHHHHHHHhCCCC---hHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 34556655443221 1123345556778999999999998874
No 19
>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=36.78 E-value=2.8e+02 Score=34.31 Aligned_cols=69 Identities=22% Similarity=0.185 Sum_probs=53.5
Q ss_pred CCcHHHHHHhhhCCCCCCCCChHHHHHHHHcCCCchhhHHHHhhccCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHH
Q 003705 281 QADEALQEACHLLPEISGPTTHPKIAQVLLERENPEAALMVLRWSGRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQR 360 (801)
Q Consensus 281 h~d~aleeA~~LLP~is~P~~h~kIlqvLl~~g~~~~AL~ylr~~g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R 360 (801)
+.|+ +.|-..||.|. ..++.+++.-|-.+|-++.||.+.-- | --...++|.-|.+.+|+..++
T Consensus 599 rrd~--~~a~~vLp~I~-k~~rt~va~Fle~~g~~e~AL~~s~D------~--------d~rFelal~lgrl~iA~~la~ 661 (794)
T KOG0276|consen 599 RRDL--EVADGVLPTIP-KEIRTKVAHFLESQGMKEQALELSTD------P--------DQRFELALKLGRLDIAFDLAV 661 (794)
T ss_pred hccc--cccccccccCc-hhhhhhHHhHhhhccchHhhhhcCCC------h--------hhhhhhhhhcCcHHHHHHHHH
Confidence 6677 88888999987 56788999988899999999974311 1 135667888999999999998
Q ss_pred hhchHH
Q 003705 361 MLCTKV 366 (801)
Q Consensus 361 ~~~~~~ 366 (801)
...+..
T Consensus 662 e~~s~~ 667 (794)
T KOG0276|consen 662 EANSEV 667 (794)
T ss_pred hhcchH
Confidence 765543
No 20
>PF10191 COG7: Golgi complex component 7 (COG7); InterPro: IPR019335 The conserved oligomeric Golgi (COG) complex is an eight-subunit (Cog1-8) peripheral Golgi protein involved in membrane trafficking and glycoconjugate synthesis []. COG7 is required for normal Golgi morphology and trafficking. Mutation in COG7 causes a congenital disorder of glycosylation [].
Probab=36.20 E-value=1.6e+02 Score=36.78 Aligned_cols=124 Identities=17% Similarity=0.277 Sum_probs=72.0
Q ss_pred HHHHHHHHhhh-hhHHHHHHHHHHHHHHHHHhhH------HHHHHHHhhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 003705 32 IIAELKLIYNL-EVEVMKTRLSLLLKFQMKLRDI------SSVIEVLASSFKDDLSAQVHDLHHFQESILKTKQHLEIMM 104 (801)
Q Consensus 32 ~~sel~~I~~~-~~~~~~~~l~~L~~~~~qL~~L------s~Vl~~L~~~~k~~~s~~l~DL~~l~e~i~~~~Qy~eVl~ 104 (801)
+.++++.+|.. +....+.+|..+++|-..|.++ ...++.|..++...+++.+...=+.+. +..++.|..|..
T Consensus 133 l~~~v~~~~~~~d~~~~a~~l~~m~~sL~~l~~~pd~~~r~~~le~l~nrLEa~vsp~Lv~al~~~~-~~~~~~~~~if~ 211 (766)
T PF10191_consen 133 LSAEVDDLFESGDIAKIADRLAEMQRSLAVLQDVPDYEERRQQLEALKNRLEALVSPQLVQALNSRD-VDAAKEYVKIFS 211 (766)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHHHHHHhhHHHHHHHHhcC-HHHHHHHHHHHH
Confidence 33556667643 4566788888888887766665 344555555555555555544322222 344555554432
Q ss_pred HHHhhccccccccccccchhhHHHHHHHHHHHhhhcccCCCcCCccccccCC--cchHHHHHHhhchh
Q 003705 105 WCAKQQFLENVRSRHASFTSWHSLVRQRKSAATERAWYDPVNYSAESTKQDG--SLFIEDALANLEIE 170 (801)
Q Consensus 105 W~~r~gLLpev~sry~~~~~w~s~vr~RK~~a~~r~w~~~~~~s~~~~~~~g--~LFID~LL~~Lgi~ 170 (801)
..+|.+.+..||..+|+ ..+.+.|-++...... ..... .-|.|.+|..+.-+
T Consensus 212 ----------~i~R~~~l~~~Y~~~r~---~~l~~~W~~~~~~~~~-~~~~~~L~~fyd~ll~~l~~E 265 (766)
T PF10191_consen 212 ----------SIGREPQLEQYYCKCRK---APLQRLWQEYCQSDQS-QSFAEWLPSFYDELLSLLHQE 265 (766)
T ss_pred ----------HcCCHHHHHHHHHHHHH---HHHHHHHHHHhhhccc-hhHHHHHHHHHHHHHHHHHHH
Confidence 24788888888888763 4557788555444422 11111 35888888876554
No 21
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=33.97 E-value=7.4e+02 Score=29.12 Aligned_cols=105 Identities=10% Similarity=-0.012 Sum_probs=53.8
Q ss_pred hhHHHHHHhHhCCChhhH--HHHhHhhhccCCCcHHHHHHhhhCCC-----CCCCCChHHHHHHHHcCCCchhhHHHHhh
Q 003705 252 RHIVDDFAATFSITRHSL--LESLTFYLLDDQADEALQEACHLLPE-----ISGPTTHPKIAQVLLERENPEAALMVLRW 324 (801)
Q Consensus 252 ~~lle~Fa~tF~Ip~~~~--~~iqgfWlLDdh~d~aleeA~~LLP~-----is~P~~h~kIlqvLl~~g~~~~AL~ylr~ 324 (801)
+..+..|.....+.+.+. ....|..+.. .+++ ++|..++-. ...+.....++..++..|+++.|+.++..
T Consensus 278 ~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~-~g~~--~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~ 354 (899)
T TIGR02917 278 EDARETLQDALKSAPEYLPALLLAGASEYQ-LGNL--EQAYQYLNQILKYAPNSHQARRLLASIQLRLGRVDEAIATLSP 354 (899)
T ss_pred HHHHHHHHHHHHhCCCchhHHHHHHHHHHH-cCCH--HHHHHHHHHHHHhCCCChHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence 344556666655555432 2233444444 4555 444443311 01122233356677788888888877765
Q ss_pred ccCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHHhh
Q 003705 325 SGRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQRML 362 (801)
Q Consensus 325 ~g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~~ 362 (801)
.-.. .| ....-......+.+..|...+|..+.+..
T Consensus 355 ~~~~-~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~ 389 (899)
T TIGR02917 355 ALGL-DP--DDPAALSLLGEAYLALGDFEKAAEYLAKA 389 (899)
T ss_pred HHhc-CC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 4211 12 11222233445667778888888776553
No 22
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=33.20 E-value=6.7e+02 Score=29.84 Aligned_cols=23 Identities=13% Similarity=0.120 Sum_probs=18.5
Q ss_pred HHHHHHHhhcChhHHHHHHHHhh
Q 003705 446 LLVVFYIQRYRYAEAYQVNLKLQ 468 (801)
Q Consensus 446 LLlVyyLQR~RYiEAvqv~~kL~ 468 (801)
.+--.|++.|+|.||+....+.-
T Consensus 547 ~la~~~~~~g~~~eAi~~~e~A~ 569 (615)
T TIGR00990 547 TMAQLLLQQGDVDEALKLFERAA 569 (615)
T ss_pred HHHHHHHHccCHHHHHHHHHHHH
Confidence 34556789999999999888764
No 23
>KOG4182 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.43 E-value=1.6e+02 Score=35.15 Aligned_cols=92 Identities=14% Similarity=0.167 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHh-hhhhHHHHHHHHHHHHHHH---HHhhH---HHHHHHHhhhhcchhhHHHHHHHHHHHHHHHHHHHHH
Q 003705 29 FKNIIAELKLIY-NLEVEVMKTRLSLLLKFQM---KLRDI---SSVIEVLASSFKDDLSAQVHDLHHFQESILKTKQHLE 101 (801)
Q Consensus 29 ~~~~~sel~~I~-~~~~~~~~~~l~~L~~~~~---qL~~L---s~Vl~~L~~~~k~~~s~~l~DL~~l~e~i~~~~Qy~e 101 (801)
+-++.+++.+.| ..+..+...+|-.|++|-. +|.+. ..-++.+..+......+.+.|.-...+ .-..||+.
T Consensus 134 l~nL~a~lED~Fa~gDL~~aadkLaalqkcL~A~~elaefAe~qkQlE~~edRLEAlaqPrltda~a~~k--td~AQd~r 211 (828)
T KOG4182|consen 134 LGNLLAELEDGFARGDLKGAADKLAALQKCLHAQEELAEFAERQKQLEDFEDRLEALAQPRLTDAFAEGK--TDQAQDFR 211 (828)
T ss_pred HHHHHHHHHHHhhcCCchhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHcCchHHHHHHccC--hHHHHHHH
Confidence 345556666666 4455667788888888864 22222 223444444444444444444322211 11245555
Q ss_pred HHHHHHhhccccccccccccchhhHHHHHH
Q 003705 102 IMMWCAKQQFLENVRSRHASFTSWHSLVRQ 131 (801)
Q Consensus 102 Vl~W~~r~gLLpev~sry~~~~~w~s~vr~ 131 (801)
++ |+|. .|+..++.+|+.|++
T Consensus 212 ~I--~irI-------gRfkqLelqY~~Vq~ 232 (828)
T KOG4182|consen 212 QI--FIRI-------GRFKQLELQYRAVQK 232 (828)
T ss_pred HH--HHHH-------hhhHHHHHHHHHHHH
Confidence 44 5653 477777888888774
No 24
>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.35 E-value=1.6e+02 Score=35.34 Aligned_cols=58 Identities=17% Similarity=0.118 Sum_probs=34.2
Q ss_pred hHHHHHHHhhcChhHHHHHHHHhhhhhhhcccCCCccHHHH--HHhHhhHHHHHHHHHHHhhhchHH
Q 003705 445 SLLVVFYIQRYRYAEAYQVNLKLQSVEQDFISKNPVSEEVL--SRMQSQIHWRTKFIDTSIELLPEV 509 (801)
Q Consensus 445 sLLlVyyLQR~RYiEAvqv~~kL~s~eq~~~~~~s~see~~--~r~r~~s~~R~~Lv~~y~~~LP~V 509 (801)
.-|--+-||||+..||+.+..+-- ++.. +++ |.+ --+++++...-.+-.+|...||++
T Consensus 541 ~tlaq~~lQ~~~i~eAielFEksa----~lAr--t~~-E~~~a~s~aeAAraq~~vtkK~~~~~~~l 600 (606)
T KOG0547|consen 541 ETLAQFELQRGKIDEAIELFEKSA----QLAR--TES-EMVHAYSLAEAARAQIAVTKKYGLTLARL 600 (606)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHH----HHHH--hHH-HHHHHHHHHHHHhhhHHHHHHhcccHHhh
Confidence 345568899999999999988742 1111 122 221 123455544455666677766654
No 25
>PRK12370 invasion protein regulator; Provisional
Probab=30.82 E-value=7e+02 Score=29.51 Aligned_cols=176 Identities=10% Similarity=-0.008 Sum_probs=0.0
Q ss_pred hhhHHHHHHhHhCCChhhHHHHhHhhh----------ccCCCcHHHHHHhhhC-----CCCCCCCChHHHHHHHHcCCCc
Q 003705 251 WRHIVDDFAATFSITRHSLLESLTFYL----------LDDQADEALQEACHLL-----PEISGPTTHPKIAQVLLERENP 315 (801)
Q Consensus 251 ~~~lle~Fa~tF~Ip~~~~~~iqgfWl----------LDdh~d~aleeA~~LL-----P~is~P~~h~kIlqvLl~~g~~ 315 (801)
++..+.-|..+..+.|++.....+.-. .+..+++ ++|...+ =....+..|-....++...|++
T Consensus 277 ~~~A~~~~~~Al~ldP~~a~a~~~La~~~~~~~~~g~~~~~~~~--~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~~ 354 (553)
T PRK12370 277 LQQALKLLTQCVNMSPNSIAPYCALAECYLSMAQMGIFDKQNAM--IKAKEHAIKATELDHNNPQALGLLGLINTIHSEY 354 (553)
T ss_pred HHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHcCCcccchHH--HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHccCH
Q ss_pred hhhHHHHhhccCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHHhhchHHHhhhhccCCcCccccccccCccchHHHHH
Q 003705 316 EAALMVLRWSGRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQRMLCTKVREKKLKFGTIGETFDDLQGGFKTWEQWLE 395 (801)
Q Consensus 316 ~~AL~ylr~~g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~~~~~~~e~~~~~~~~~~~~~~~~~~~~~w~~~~E 395 (801)
+.|+.+++..- .-...+..-....-.+++..|..-||..+.++...--.. ..
T Consensus 355 ~~A~~~~~~Al---~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~-------------------------~~ 406 (553)
T PRK12370 355 IVGSLLFKQAN---LLSPISADIKYYYGWNLFMAGQLEEALQTINECLKLDPT-------------------------RA 406 (553)
T ss_pred HHHHHHHHHHH---HhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-------------------------Ch
Q ss_pred HHHHHHHHhhhhcchHHHhhcCCCChhhHHHHHHHhccCCCCCCCCCcchHHHHHHHhhcChhHHHHHHHHh
Q 003705 396 VLVTEICCLCIRRNLVDRMIELPWNTDEEKYLHKCLLDSATDDPSTTVGSLLVVFYIQRYRYAEAYQVNLKL 467 (801)
Q Consensus 396 ~Ll~~~f~~C~~~~~l~~LL~LPLd~eEEe~L~k~L~~~~~~~p~~~~~sLLlVyyLQR~RYiEAvqv~~kL 467 (801)
.............+..+ +=.+++.+.|.......+ ....++-..|.+.||+.||.+..+++
T Consensus 407 ~~~~~~~~~~~~~g~~e---------eA~~~~~~~l~~~~p~~~--~~~~~la~~l~~~G~~~eA~~~~~~~ 467 (553)
T PRK12370 407 AAGITKLWITYYHTGID---------DAIRLGDELRSQHLQDNP--ILLSMQVMFLSLKGKHELARKLTKEI 467 (553)
T ss_pred hhHHHHHHHHHhccCHH---------HHHHHHHHHHHhccccCH--HHHHHHHHHHHhCCCHHHHHHHHHHh
No 26
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=30.26 E-value=5.8e+02 Score=33.11 Aligned_cols=82 Identities=17% Similarity=0.003 Sum_probs=49.0
Q ss_pred hHhhhccCCCcHHHHHHhhhCC-----CCCCCCChHHHHHHHHcCCCchhhHHHHhhc-cCCCCCCccChHHHHHHH-HH
Q 003705 273 LTFYLLDDQADEALQEACHLLP-----EISGPTTHPKIAQVLLERENPEAALMVLRWS-GRDGGSLLVSLSEAVTAV-RI 345 (801)
Q Consensus 273 qgfWlLDdh~d~aleeA~~LLP-----~is~P~~h~kIlqvLl~~g~~~~AL~ylr~~-g~~~~P~l~slsEA~l~l-~V 345 (801)
+|-.++. .+++ ++|+..+- ....||.+-.+..++...|+++.|+.+++.. ... |. .. ++...+ ..
T Consensus 467 ~a~~~~~-~g~~--~eA~~~~~~Al~~~P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~--P~--~~-~~~~a~al~ 538 (1157)
T PRK11447 467 QAEALEN-QGKW--AQAAELQRQRLALDPGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQK--PN--DP-EQVYAYGLY 538 (1157)
T ss_pred HHHHHHH-CCCH--HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CC--CH-HHHHHHHHH
Confidence 4445565 6666 55544431 1224677788899999999999999887754 211 21 12 222222 23
Q ss_pred HHhcCChhHHHHHHHhh
Q 003705 346 RVECALLTEAFTYQRML 362 (801)
Q Consensus 346 lLan~lItEAF~~~R~~ 362 (801)
+.+.+...+|..+.+..
T Consensus 539 l~~~~~~~~Al~~l~~l 555 (1157)
T PRK11447 539 LSGSDRDRAALAHLNTL 555 (1157)
T ss_pred HHhCCCHHHHHHHHHhC
Confidence 44567778888877654
No 27
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=29.66 E-value=1.1e+03 Score=29.28 Aligned_cols=103 Identities=14% Similarity=0.068 Sum_probs=57.8
Q ss_pred hhhHHHHHHhHhCCChh--hHHHHhHhhhccCCCcHHHHHHhhhCCC-----CCCCCChHHHHHHHHcCCCchhhHHHHh
Q 003705 251 WRHIVDDFAATFSITRH--SLLESLTFYLLDDQADEALQEACHLLPE-----ISGPTTHPKIAQVLLERENPEAALMVLR 323 (801)
Q Consensus 251 ~~~lle~Fa~tF~Ip~~--~~~~iqgfWlLDdh~d~aleeA~~LLP~-----is~P~~h~kIlqvLl~~g~~~~AL~ylr 323 (801)
|...+.-|.....+.|. ......+..+++ .+++ ++|+.+|-. ...+. +..+..++...|+++.|+.+++
T Consensus 65 ~~~A~~~~~~al~~~P~~~~a~~~la~~l~~-~g~~--~eA~~~l~~~l~~~P~~~~-~~~la~~l~~~g~~~~Al~~l~ 140 (765)
T PRK10049 65 WQNSLTLWQKALSLEPQNDDYQRGLILTLAD-AGQY--DEALVKAKQLVSGAPDKAN-LLALAYVYKRAGRHWDELRAMT 140 (765)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-CCCH--HHHHHHHHHHHHhCCCCHH-HHHHHHHHHHCCCHHHHHHHHH
Confidence 44556677777777443 234566667777 7776 666665522 11224 5556777888999999997775
Q ss_pred hc-cCCCCCCccChHHHHHHH-HHHHhcCChhHHHHHHHhh
Q 003705 324 WS-GRDGGSLLVSLSEAVTAV-RIRVECALLTEAFTYQRML 362 (801)
Q Consensus 324 ~~-g~~~~P~l~slsEA~l~l-~VlLan~lItEAF~~~R~~ 362 (801)
.. ... | . ..++...+ .++..++..-+|+......
T Consensus 141 ~al~~~--P--~-~~~~~~~la~~l~~~~~~e~Al~~l~~~ 176 (765)
T PRK10049 141 QALPRA--P--Q-TQQYPTEYVQALRNNRLSAPALGAIDDA 176 (765)
T ss_pred HHHHhC--C--C-CHHHHHHHHHHHHHCCChHHHHHHHHhC
Confidence 43 221 3 1 22333333 3344445555577555443
No 28
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=29.30 E-value=56 Score=34.27 Aligned_cols=109 Identities=17% Similarity=0.103 Sum_probs=58.3
Q ss_pred hhhHHHHHHhHhCCChhh--HHHHhHhhhccCCCcH-HHHHHhhhCCC--CCCCCChHHHHHHHHcCCCchhhHHHHhhc
Q 003705 251 WRHIVDDFAATFSITRHS--LLESLTFYLLDDQADE-ALQEACHLLPE--ISGPTTHPKIAQVLLERENPEAALMVLRWS 325 (801)
Q Consensus 251 ~~~lle~Fa~tF~Ip~~~--~~~iqgfWlLDdh~d~-aleeA~~LLP~--is~P~~h~kIlqvLl~~g~~~~AL~ylr~~ 325 (801)
++..+..|..+..+.|.. +....++.++| .+++ .+.+++..+-. ...|.+...+..+++..|+++.||.+++..
T Consensus 162 ~~~A~~~~~~al~~~P~~~~~~~~l~~~li~-~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~ 240 (280)
T PF13429_consen 162 PDKALRDYRKALELDPDDPDARNALAWLLID-MGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKA 240 (280)
T ss_dssp HHHHHHHHHHHHHH-TT-HHHHHHHHHHHCT-TCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhcccccccccccccccc
Confidence 346678888888888863 34444556666 8877 23345544411 245677788999999999999999888764
Q ss_pred cCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHHhhc
Q 003705 326 GRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQRMLC 363 (801)
Q Consensus 326 g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~~~ 363 (801)
-.- ....+.-...+-.++...|..-||+.+.|+.-
T Consensus 241 ~~~---~p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~ 275 (280)
T PF13429_consen 241 LKL---NPDDPLWLLAYADALEQAGRKDEALRLRRQAL 275 (280)
T ss_dssp HHH---STT-HHHHHHHHHHHT----------------
T ss_pred ccc---cccccccccccccccccccccccccccccccc
Confidence 210 12223344567788999999999999887653
No 29
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=26.93 E-value=8.9e+02 Score=30.82 Aligned_cols=93 Identities=23% Similarity=0.158 Sum_probs=58.6
Q ss_pred hCCChhhHHHHhHhhhccCCCcHHHHHHhhhCCCCCCCCChHHHHHHHHcCCCchhhH-HHHhhccCCCCCC-----ccC
Q 003705 262 FSITRHSLLESLTFYLLDDQADEALQEACHLLPEISGPTTHPKIAQVLLERENPEAAL-MVLRWSGRDGGSL-----LVS 335 (801)
Q Consensus 262 F~Ip~~~~~~iqgfWlLDdh~d~aleeA~~LLP~is~P~~h~kIlqvLl~~g~~~~AL-~ylr~~g~~~~P~-----l~s 335 (801)
+.-....--.+.++|+|.+-++ |+....-||+-+ .+-|++.+.|.+.|--+.|. .|+|..- |. +..
T Consensus 819 Y~~~~~~e~~~ecly~le~f~~--LE~la~~Lpe~s--~llp~~a~mf~svGMC~qAV~a~Lr~s~----pkaAv~tCv~ 890 (1189)
T KOG2041|consen 819 YSYCGDTENQIECLYRLELFGE--LEVLARTLPEDS--ELLPVMADMFTSVGMCDQAVEAYLRRSL----PKAAVHTCVE 890 (1189)
T ss_pred HHhccchHhHHHHHHHHHhhhh--HHHHHHhcCccc--chHHHHHHHHHhhchHHHHHHHHHhccC----cHHHHHHHHH
Confidence 3344555667889999974444 466666777643 35677888888888777776 5666541 20 111
Q ss_pred h---------------HHHHH----HHHHHHhcCChhHHHHHHHhh
Q 003705 336 L---------------SEAVT----AVRIRVECALLTEAFTYQRML 362 (801)
Q Consensus 336 l---------------sEA~l----~l~VlLan~lItEAF~~~R~~ 362 (801)
+ .++.+ +-.-+|+-++..||+...|+.
T Consensus 891 LnQW~~avelaq~~~l~qv~tliak~aaqll~~~~~~eaIe~~Rka 936 (1189)
T KOG2041|consen 891 LNQWGEAVELAQRFQLPQVQTLIAKQAAQLLADANHMEAIEKDRKA 936 (1189)
T ss_pred HHHHHHHHHHHHhccchhHHHHHHHHHHHHHhhcchHHHHHHhhhc
Confidence 1 11111 334478888999999999974
No 30
>PF10293 DUF2405: Domain of unknown function (DUF2405); InterPro: IPR019409 The function of the FMP27 protein is not known. FMP27 is the product of a nuclear encoded gene but it is detected in highly purified mitochondria in high-throughput studies []. This entry represents a conserved region found within FMP27.
Probab=26.75 E-value=1e+02 Score=31.11 Aligned_cols=33 Identities=30% Similarity=0.472 Sum_probs=29.0
Q ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHHhhHH
Q 003705 33 IAELKLIYNLEVEVMKTRLSLLLKFQMKLRDIS 65 (801)
Q Consensus 33 ~sel~~I~~~~~~~~~~~l~~L~~~~~qL~~Ls 65 (801)
+++|.+||.+|..|-++|+..++.+..+++.+.
T Consensus 119 E~~L~~Iy~lGl~Eq~~Rl~r~~~Fe~k~~~~~ 151 (157)
T PF10293_consen 119 ESELGMIYRLGLDEQRERLEREEAFEEKVKKIR 151 (157)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999888888777654
No 31
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=26.60 E-value=3.2e+02 Score=26.00 Aligned_cols=98 Identities=18% Similarity=0.139 Sum_probs=59.4
Q ss_pred HHHHHhHhCCC--hhhHHHHhHhhhccCCCcHHHHHHhhhCCCC---C-CC----CChHHHHHHHHcCCCchhhHHHHhh
Q 003705 255 VDDFAATFSIT--RHSLLESLTFYLLDDQADEALQEACHLLPEI---S-GP----TTHPKIAQVLLERENPEAALMVLRW 324 (801)
Q Consensus 255 le~Fa~tF~Ip--~~~~~~iqgfWlLDdh~d~aleeA~~LLP~i---s-~P----~~h~kIlqvLl~~g~~~~AL~ylr~ 324 (801)
++.|...+.=+ .....+..+--+++ -+++ ++|...|-.+ . .| .-.-.++.+++..|+++.|+..+..
T Consensus 34 ~~~l~~~~~~s~ya~~A~l~lA~~~~~-~g~~--~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 34 AEQLAKDYPSSPYAALAALQLAKAAYE-QGDY--DEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEALATLQQ 110 (145)
T ss_pred HHHHHHHCCCChHHHHHHHHHHHHHHH-CCCH--HHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence 34455544444 23444555555566 7777 7777766221 1 11 2233478899999999999999977
Q ss_pred ccCCCCCCccChHHHHHHHHHHHhcCChhHHHHHH
Q 003705 325 SGRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQ 359 (801)
Q Consensus 325 ~g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~ 359 (801)
... ++. ...-..+.=.|++..|...+|...=
T Consensus 111 ~~~---~~~-~~~~~~~~Gdi~~~~g~~~~A~~~y 141 (145)
T PF09976_consen 111 IPD---EAF-KALAAELLGDIYLAQGDYDEARAAY 141 (145)
T ss_pred ccC---cch-HHHHHHHHHHHHHHCCCHHHHHHHH
Confidence 531 222 2333445566788888888887643
No 32
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=25.83 E-value=84 Score=22.82 Aligned_cols=30 Identities=20% Similarity=0.266 Sum_probs=20.2
Q ss_pred HHHHHHHhhcChhHHHHHHHHhhhhhhhcc
Q 003705 446 LLVVFYIQRYRYAEAYQVNLKLQSVEQDFI 475 (801)
Q Consensus 446 LLlVyyLQR~RYiEAvqv~~kL~s~eq~~~ 475 (801)
-|-.+|..+|+|.||..+.++.-.+.+.+.
T Consensus 7 ~la~~~~~~g~~~~A~~~~~~al~~~~~~~ 36 (42)
T PF13374_consen 7 NLANAYRAQGRYEEALELLEEALEIRERLL 36 (42)
T ss_dssp HHHHHHHHCT-HHHHHHHHHHHHHHH----
T ss_pred HHHHHHHhhhhcchhhHHHHHHHHHHHHHh
Confidence 456778888999999999998865544443
No 33
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=25.46 E-value=9.2e+02 Score=31.36 Aligned_cols=73 Identities=15% Similarity=0.173 Sum_probs=43.4
Q ss_pred hhhHHHHHHhHhCCChhhHHHHhHhhhccC--CCcHHHHHHhhhCCC-----CCCCCChHHHHHHHHcCCCchhhHHHHh
Q 003705 251 WRHIVDDFAATFSITRHSLLESLTFYLLDD--QADEALQEACHLLPE-----ISGPTTHPKIAQVLLERENPEAALMVLR 323 (801)
Q Consensus 251 ~~~lle~Fa~tF~Ip~~~~~~iqgfWlLDd--h~d~aleeA~~LLP~-----is~P~~h~kIlqvLl~~g~~~~AL~ylr 323 (801)
++..+..|...|...+....+...||.+=- .++. ++|+..|-. ...+..+-.+..++...|+++.|+.++.
T Consensus 128 ~~eA~~~~~~~l~~~p~~~~la~~y~~~~~~~~g~~--~~A~~~L~~ll~~~P~~~~~~~~LA~ll~~~g~~~eAl~~l~ 205 (1157)
T PRK11447 128 TEEALASYDKLFNGAPPELDLAVEYWRLVAKLPAQR--PEAINQLQRLNADYPGNTGLRNTLALLLFSSGRRDEGFAVLE 205 (1157)
T ss_pred HHHHHHHHHHHccCCCCChHHHHHHHHHHhhCCccH--HHHHHHHHHHHHhCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Confidence 445667777777775544444445555410 2333 444444411 1123345567888889999999999887
Q ss_pred hc
Q 003705 324 WS 325 (801)
Q Consensus 324 ~~ 325 (801)
..
T Consensus 206 ~~ 207 (1157)
T PRK11447 206 QM 207 (1157)
T ss_pred HH
Confidence 65
No 34
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=25.20 E-value=1.2e+03 Score=28.35 Aligned_cols=103 Identities=10% Similarity=0.053 Sum_probs=56.5
Q ss_pred hhHHHHHHhHhCCChhhH--HHHhHhhhccCCCcHHHHHHhhhCCC-----CCCCCChHHHHHHHHcCCCchhhHHHHhh
Q 003705 252 RHIVDDFAATFSITRHSL--LESLTFYLLDDQADEALQEACHLLPE-----ISGPTTHPKIAQVLLERENPEAALMVLRW 324 (801)
Q Consensus 252 ~~lle~Fa~tF~Ip~~~~--~~iqgfWlLDdh~d~aleeA~~LLP~-----is~P~~h~kIlqvLl~~g~~~~AL~ylr~ 324 (801)
+..+..|...-.+.|+.. ....|--++. .+++ ++|+..+-. ...++.+...+.++...|+++.|+.+++.
T Consensus 93 ~~A~~~l~~~l~~~P~~~~a~~~la~~l~~-~g~~--~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~ 169 (656)
T PRK15174 93 DAVLQVVNKLLAVNVCQPEDVLLVASVLLK-SKQY--ATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLART 169 (656)
T ss_pred HHHHHHHHHHHHhCCCChHHHHHHHHHHHH-cCCH--HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHH
Confidence 344566666666655432 2223333444 5555 444444311 12234555577788888999988877654
Q ss_pred c-cCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHHhh
Q 003705 325 S-GRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQRML 362 (801)
Q Consensus 325 ~-g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~~ 362 (801)
. ... |. ..++...+..++..|...||....+..
T Consensus 170 ~~~~~--P~---~~~a~~~~~~l~~~g~~~eA~~~~~~~ 203 (656)
T PRK15174 170 QAQEV--PP---RGDMIATCLSFLNKSRLPEDHDLARAL 203 (656)
T ss_pred HHHhC--CC---CHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 3 211 21 123333444577788888888776653
No 35
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=23.42 E-value=1.7e+03 Score=28.93 Aligned_cols=100 Identities=11% Similarity=0.007 Sum_probs=47.9
Q ss_pred HHHHhHhCCChh----hHHHHhHhhhccCCCcHH---HHHHhhhCCCCCCCCChHHHHHHHHcCCCchhhHHHHhhccCC
Q 003705 256 DDFAATFSITRH----SLLESLTFYLLDDQADEA---LQEACHLLPEISGPTTHPKIAQVLLERENPEAALMVLRWSGRD 328 (801)
Q Consensus 256 e~Fa~tF~Ip~~----~~~~iqgfWlLDdh~d~a---leeA~~LLP~is~P~~h~kIlqvLl~~g~~~~AL~ylr~~g~~ 328 (801)
+.+.......+. -.....|..+++...+.+ +.+++...|.. +.+--+..++...|+++.|+..++.....
T Consensus 462 ~~~~~al~~~p~~~~~~a~~~LG~~l~~~~~~eAi~a~~~Al~~~Pd~---~~~L~lA~al~~~Gr~eeAi~~~rka~~~ 538 (987)
T PRK09782 462 PAIVRLLGDMSPSYDAAAWNRLAKCYRDTLPGVALYAWLQAEQRQPDA---WQHRAVAYQAYQVEDYATALAAWQKISLH 538 (987)
T ss_pred HHHHHhcccCCCCCCHHHHHHHHHHHHhCCcHHHHHHHHHHHHhCCch---HHHHHHHHHHHHCCCHHHHHHHHHHHhcc
Confidence 344455554222 123445555555211111 23444444431 22333455566777777777766643211
Q ss_pred CCCCccChHHHHHHHHHHHhcCChhHHHHHHHhh
Q 003705 329 GGSLLVSLSEAVTAVRIRVECALLTEAFTYQRML 362 (801)
Q Consensus 329 ~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~~ 362 (801)
|+- .......-.+++..|...+|..+.++.
T Consensus 539 --~p~--~~a~~~la~all~~Gd~~eA~~~l~qA 568 (987)
T PRK09782 539 --DMS--NEDLLAAANTAQAAGNGAARDRWLQQA 568 (987)
T ss_pred --CCC--cHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 211 122233345566677777776666543
No 36
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=22.44 E-value=57 Score=33.63 Aligned_cols=36 Identities=28% Similarity=0.362 Sum_probs=23.1
Q ss_pred chHHHhhcCCCChhhHHHHHHHhccCCCCCCCCCcc
Q 003705 409 NLVDRMIELPWNTDEEKYLHKCLLDSATDDPSTTVG 444 (801)
Q Consensus 409 ~~l~~LL~LPLd~eEEe~L~k~L~~~~~~~p~~~~~ 444 (801)
+++..+-+||++++|++-+++||.+..|-.|+++.+
T Consensus 41 ~RM~~~hGl~Is~eer~avVkYLAd~~GLap~Et~~ 76 (167)
T PF09098_consen 41 KRMQRVHGLPISPEERRAVVKYLADTQGLAPSETAP 76 (167)
T ss_dssp HHHHHHC-----HHHHHHHHHHHHHHT---CGGCTT
T ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHccCCCchhhcc
Confidence 456667799999999999999999999988877643
No 37
>COG4755 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.20 E-value=8.3e+02 Score=24.73 Aligned_cols=79 Identities=16% Similarity=0.162 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHHHHhhHHHHHHHHhhhhcch------hhHHHHHH--------HHHHHH-HHHHHHHHHHHHHHHhhccc
Q 003705 48 KTRLSLLLKFQMKLRDISSVIEVLASSFKDD------LSAQVHDL--------HHFQES-ILKTKQHLEIMMWCAKQQFL 112 (801)
Q Consensus 48 ~~~l~~L~~~~~qL~~Ls~Vl~~L~~~~k~~------~s~~l~DL--------~~l~e~-i~~~~Qy~eVl~W~~r~gLL 112 (801)
+.||+.+.+...-|..+..+|.++.+=..+. ...-+.|+ ..+.+. |.-++||-+++.=|.|.|=|
T Consensus 44 ~DRLdLi~~~r~af~hm~rtLKaFd~WLqdP~v~s~mPremL~dv~~t~~e~~~~lielDIrHTSq~kelisk~srEGkl 123 (151)
T COG4755 44 ADRLDLIYSARAAFGHMARTLKAFDSWLQDPVVTSVMPREMLRDVESTLREVAIKLIELDIRHTSQYKELISKFSREGKL 123 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHhhhCcHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHhhcCCC
Confidence 4688888888889999999999988644442 23333342 223332 66679999999999999999
Q ss_pred cccccc--cccchhhH
Q 003705 113 ENVRSR--HASFTSWH 126 (801)
Q Consensus 113 pev~sr--y~~~~~w~ 126 (801)
|-+..- ...++.|+
T Consensus 124 ~pvl~~~~~~~~~~~r 139 (151)
T COG4755 124 PPVLMLYIQQRPQAPR 139 (151)
T ss_pred CchHHhhhhcccCchH
Confidence 998763 44566664
No 38
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=22.07 E-value=7.5e+02 Score=25.94 Aligned_cols=190 Identities=16% Similarity=0.138 Sum_probs=65.3
Q ss_pred HHHhhhccCCCCCCchhhhHHHHHHhHhCCChhhHHHHhHhhh-ccCCCcHHHHHHhhhCCC----CCCCCChHHHHHHH
Q 003705 235 FLYYLFDRHWTMPDENWRHIVDDFAATFSITRHSLLESLTFYL-LDDQADEALQEACHLLPE----ISGPTTHPKIAQVL 309 (801)
Q Consensus 235 ~lYlLLD~~~~~p~~~~~~lle~Fa~tF~Ip~~~~~~iqgfWl-LDdh~d~aleeA~~LLP~----is~P~~h~kIlqvL 309 (801)
|++++-|+.+...+. +....-|.....+++....-..-+-. +. ++++ ++|..++-. ...|-.-...++.+
T Consensus 46 ~~~~~a~La~~~~~~--~~A~~ay~~l~~~~~~~~~~~~~l~~l~~-~~~~--~~A~~~~~~~~~~~~~~~~l~~~l~~~ 120 (280)
T PF13429_consen 46 YWRLLADLAWSLGDY--DEAIEAYEKLLASDKANPQDYERLIQLLQ-DGDP--EEALKLAEKAYERDGDPRYLLSALQLY 120 (280)
T ss_dssp -----------------------------------------------------------------------------H-H
T ss_pred ccccccccccccccc--ccccccccccccccccccccccccccccc-cccc--cccccccccccccccccchhhHHHHHH
Confidence 334444555543321 23334444444555443322222222 33 6666 667666521 11232233467778
Q ss_pred HcCCCchhhHHHHhhccCCCCCCccChHHH-HHHHHHHHhcCChhHHHHHHHhhchHHHhhhhccCCcCccccccccCcc
Q 003705 310 LERENPEAALMVLRWSGRDGGSLLVSLSEA-VTAVRIRVECALLTEAFTYQRMLCTKVREKKLKFGTIGETFDDLQGGFK 388 (801)
Q Consensus 310 l~~g~~~~AL~ylr~~g~~~~P~l~slsEA-~l~l~VlLan~lItEAF~~~R~~~~~~~e~~~~~~~~~~~~~~~~~~~~ 388 (801)
...++.+.+..++...... +........ ...-.+....|..-+|..+.++....... +
T Consensus 121 ~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~---------~---------- 179 (280)
T PF13429_consen 121 YRLGDYDEAEELLEKLEEL--PAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELDPD---------D---------- 179 (280)
T ss_dssp HHTT-HHHHHHHHHHHHH---T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT--------------------
T ss_pred HHHhHHHHHHHHHHHHHhc--cCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC---------C----------
Confidence 8999999988877763211 212111111 12234567788999998888776543211 0
Q ss_pred chHHHHHHHHHHHHHhhhhcchHHHhhcCCCChhhHHHHHHHhccCCCCCCCCCcchHHHHHHHhhcChhHHHHHHHHhh
Q 003705 389 TWEQWLEVLVTEICCLCIRRNLVDRMIELPWNTDEEKYLHKCLLDSATDDPSTTVGSLLVVFYIQRYRYAEAYQVNLKLQ 468 (801)
Q Consensus 389 ~w~~~~E~Ll~~~f~~C~~~~~l~~LL~LPLd~eEEe~L~k~L~~~~~~~p~~~~~sLLlVyyLQR~RYiEAvqv~~kL~ 468 (801)
..+.......-++.+..++ -.++|..+....+. +| .....+-.-|++-|+|.+|+...+++-
T Consensus 180 ------~~~~~~l~~~li~~~~~~~---------~~~~l~~~~~~~~~-~~--~~~~~la~~~~~lg~~~~Al~~~~~~~ 241 (280)
T PF13429_consen 180 ------PDARNALAWLLIDMGDYDE---------AREALKRLLKAAPD-DP--DLWDALAAAYLQLGRYEEALEYLEKAL 241 (280)
T ss_dssp ------HHHHHHHHHHHCTTCHHHH---------HHHHHHHHHHH-HT-SC--CHCHHHHHHHHHHT-HHHHHHHHHHHH
T ss_pred ------HHHHHHHHHHHHHCCChHH---------HHHHHHHHHHHCcC-HH--HHHHHHHHHhccccccccccccccccc
Confidence 1222222222233333333 23566666655421 11 234556677888899999999999985
No 39
>KOG2180 consensus Late Golgi protein sorting complex, subunit Vps53 [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.56 E-value=7.1e+02 Score=31.38 Aligned_cols=16 Identities=31% Similarity=0.542 Sum_probs=12.5
Q ss_pred HHHHHHHHHHhhcccc
Q 003705 98 QHLEIMMWCAKQQFLE 113 (801)
Q Consensus 98 Qy~eVl~W~~r~gLLp 113 (801)
--.+++.|||++.|-+
T Consensus 229 vreelIkwf~~qqL~e 244 (793)
T KOG2180|consen 229 VREELIKWFCSQQLEE 244 (793)
T ss_pred cHHHHHHHHHHHHHHH
Confidence 4567899999988755
No 40
>KOG4521 consensus Nuclear pore complex, Nup160 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.51 E-value=1.2e+03 Score=31.27 Aligned_cols=136 Identities=17% Similarity=0.167 Sum_probs=87.6
Q ss_pred hHHHHHHHHcCCCchhhHHHHhhc-cCCCCCCccChHHHHH---HHHHHHhcCChhHHHHHHHhhchHHHhhhhccCCcC
Q 003705 302 HPKIAQVLLERENPEAALMVLRWS-GRDGGSLLVSLSEAVT---AVRIRVECALLTEAFTYQRMLCTKVREKKLKFGTIG 377 (801)
Q Consensus 302 h~kIlqvLl~~g~~~~AL~ylr~~-g~~~~P~l~slsEA~l---~l~VlLan~lItEAF~~~R~~~~~~~e~~~~~~~~~ 377 (801)
..++++-|=..+-++.+.+++... .. -+....+.|.+ ...-.|..|+..+|+...=+.++.-++ +
T Consensus 986 Ylkv~rlle~hn~~E~vcQlA~~AIe~---l~dd~ps~a~~~t~vFnhhldlgh~~qAy~ai~~npdserr-r------- 1054 (1480)
T KOG4521|consen 986 YLKVVRLLEEHNHAEEVCQLAVKAIEN---LPDDNPSVALISTTVFNHHLDLGHWFQAYKAILRNPDSERR-R------- 1054 (1480)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHHHHh---CCCcchhHHHHHHHHHHhhhchhhHHHHHHHHHcCCcHHHH-H-------
Confidence 456788777888887776554432 11 11222333333 233467788899999877666653221 1
Q ss_pred ccccccccCccchHHHHHHHHHHHHHhhhhcchHHHhhcCCCChhhHHHHHHHhccCCCCCCC---CCcchHHHHHHHhh
Q 003705 378 ETFDDLQGGFKTWEQWLEVLVTEICCLCIRRNLVDRMIELPWNTDEEKYLHKCLLDSATDDPS---TTVGSLLVVFYIQR 454 (801)
Q Consensus 378 ~~~~~~~~~~~~w~~~~E~Ll~~~f~~C~~~~~l~~LL~LPLd~eEEe~L~k~L~~~~~~~p~---~~~~sLLlVyyLQR 454 (801)
+-+++||--+|+ | +.++.|.++||=.-|++ ++.+|.+.++..-. ...=+||-.||..|
T Consensus 1055 --------------dcLRqlvivLfe-c---g~l~~L~~fpfigl~~e-ve~~l~esaaRs~~~mk~nyYelLYAfh~~R 1115 (1480)
T KOG4521|consen 1055 --------------DCLRQLVIVLFE-C---GELEALATFPFIGLEQE-VEDFLRESAARSSPSMKKNYYELLYAFHVAR 1115 (1480)
T ss_pred --------------HHHHHHHHHHHh-c---cchHHHhhCCccchHHH-HHHHHHHHHhhcCccccccHHHHHHHHHHhh
Confidence 135777766664 3 56788999999888776 46667666654321 12557999999999
Q ss_pred cChhHHHHHHHHh
Q 003705 455 YRYAEAYQVNLKL 467 (801)
Q Consensus 455 ~RYiEAvqv~~kL 467 (801)
++|--|--+....
T Consensus 1116 hN~RkaatvMYEy 1128 (1480)
T KOG4521|consen 1116 HNFRKAATVMYEY 1128 (1480)
T ss_pred cchhHHHHHHHHH
Confidence 9999998777655
No 41
>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.50 E-value=4.7e+02 Score=33.01 Aligned_cols=93 Identities=17% Similarity=0.133 Sum_probs=68.1
Q ss_pred HHHHHhHhCCChhhHHHHhHhhhccCCCcHHHHHHhhhCCCC-CCC-CChHHHHHHHHcCCCchhhHHHHhhccCCCCCC
Q 003705 255 VDDFAATFSITRHSLLESLTFYLLDDQADEALQEACHLLPEI-SGP-TTHPKIAQVLLERENPEAALMVLRWSGRDGGSL 332 (801)
Q Consensus 255 le~Fa~tF~Ip~~~~~~iqgfWlLDdh~d~aleeA~~LLP~i-s~P-~~h~kIlqvLl~~g~~~~AL~ylr~~g~~~~P~ 332 (801)
+++..+.|.||.+-+-..+.+-|-| -.+. +.++-+..- ..| .+.| ++++.+.+|+.+.|..|+-..+ +
T Consensus 703 a~ql~~~FkipdKr~~wLk~~aLa~-~~kw---eeLekfAkskksPIGy~P-FVe~c~~~~n~~EA~KYiprv~-----~ 772 (829)
T KOG2280|consen 703 AEQLKSDFKIPDKRLWWLKLTALAD-IKKW---EELEKFAKSKKSPIGYLP-FVEACLKQGNKDEAKKYIPRVG-----G 772 (829)
T ss_pred HHHHHHhcCCcchhhHHHHHHHHHh-hhhH---HHHHHHHhccCCCCCchh-HHHHHHhcccHHHHhhhhhccC-----C
Confidence 6788999999999888888888887 6665 333333222 226 5555 7999999999999999986653 1
Q ss_pred ccChHHHHHHHHHHHhcCChhHHHHHHHhhc
Q 003705 333 LVSLSEAVTAVRIRVECALLTEAFTYQRMLC 363 (801)
Q Consensus 333 l~slsEA~l~l~VlLan~lItEAF~~~R~~~ 363 (801)
+. ..+...+++|.+.||...+=.+.
T Consensus 773 l~------ekv~ay~~~~~~~eAad~A~~~r 797 (829)
T KOG2280|consen 773 LQ------EKVKAYLRVGDVKEAADLAAEHR 797 (829)
T ss_pred hH------HHHHHHHHhccHHHHHHHHHHhc
Confidence 32 35666888999999998875543
No 42
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=21.31 E-value=7.1e+02 Score=23.61 Aligned_cols=59 Identities=8% Similarity=-0.129 Sum_probs=35.9
Q ss_pred ChHHHHHHHHcCCCchhhHHHHhhc-cCCCCCCccChHHHHHHHHHHHhcCChhHHHHHHHhhc
Q 003705 301 THPKIAQVLLERENPEAALMVLRWS-GRDGGSLLVSLSEAVTAVRIRVECALLTEAFTYQRMLC 363 (801)
Q Consensus 301 ~h~kIlqvLl~~g~~~~AL~ylr~~-g~~~~P~l~slsEA~l~l~VlLan~lItEAF~~~R~~~ 363 (801)
.+..+..++...|+++.|+.+++.. ... |. ...-......+....|...+|..+.+...
T Consensus 67 ~~~~la~~~~~~~~~~~A~~~~~~al~~~--~~--~~~~~~~~~~~~~~~g~~~~A~~~~~~~~ 126 (234)
T TIGR02521 67 AYLALALYYQQLGELEKAEDSFRRALTLN--PN--NGDVLNNYGTFLCQQGKYEQAMQQFEQAI 126 (234)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CC--CHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence 3444667777899999999776543 211 21 11122233455677788888887776653
Done!