Query 008526
Match_columns 563
No_of_seqs 144 out of 175
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 13:16:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008526.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008526hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3849 GDP-fucose protein O-f 100.0 2.4E-84 5.2E-89 646.8 16.3 291 201-548 18-375 (386)
2 PF10250 O-FucT: GDP-fucose pr 100.0 3.2E-47 6.8E-52 381.5 7.5 290 216-544 1-346 (351)
3 PF05830 NodZ: Nodulation prot 98.2 6E-06 1.3E-10 85.9 10.2 138 384-534 144-292 (321)
4 PF01531 Glyco_transf_11: Glyc 97.9 7.4E-05 1.6E-09 76.2 11.5 103 405-537 162-266 (298)
5 KOG3705 Glycoprotein 6-alpha-L 92.6 0.17 3.6E-06 55.4 5.1 132 405-554 361-507 (580)
6 PF03254 XG_FTase: Xyloglucan 90.9 3 6.5E-05 46.7 12.5 139 383-537 275-436 (476)
7 PRK07283 hypothetical protein; 74.6 12 0.00027 33.0 6.9 44 438-483 24-67 (98)
8 PRK06683 hypothetical protein; 70.6 8.8 0.00019 33.2 4.9 44 438-483 17-60 (82)
9 PRK13601 putative L7Ae-like ri 66.2 13 0.00028 32.3 5.0 44 438-483 14-57 (82)
10 PRK13600 putative ribosomal pr 64.2 15 0.00032 32.3 5.0 45 438-484 19-63 (84)
11 COG2879 Uncharacterized small 63.9 3.1 6.7E-05 35.1 0.8 26 258-285 25-50 (65)
12 PRK13602 putative ribosomal pr 58.6 19 0.00041 31.0 4.7 44 438-483 17-60 (82)
13 PRK09375 quinolinate synthetas 53.3 64 0.0014 34.7 8.5 107 339-471 144-262 (319)
14 PRK07714 hypothetical protein; 50.1 39 0.00085 29.8 5.4 44 438-483 24-67 (100)
15 PTZ00106 60S ribosomal protein 47.2 34 0.00073 31.1 4.6 42 438-481 31-72 (108)
16 PRK01018 50S ribosomal protein 47.1 38 0.00081 30.1 4.8 43 438-482 22-64 (99)
17 cd01028 TOPRIM_TopoIA TOPRIM_T 42.7 28 0.00061 32.1 3.5 26 433-460 77-102 (142)
18 PF09580 Spore_YhcN_YlaJ: Spor 41.3 63 0.0014 30.6 5.7 49 407-470 102-152 (177)
19 TIGR03609 S_layer_CsaB polysac 41.0 1.3E+02 0.0028 30.5 8.2 58 405-471 171-230 (298)
20 cd03362 TOPRIM_TopoIA_TopoIII 39.8 34 0.00074 32.0 3.6 26 433-460 85-110 (151)
21 TIGR02201 heptsyl_trn_III lipo 38.9 1.8E+02 0.004 29.9 9.1 58 389-456 163-221 (344)
22 PF02348 CTP_transf_3: Cytidyl 38.6 1.3E+02 0.0029 28.5 7.5 24 435-458 26-49 (217)
23 PRK05583 ribosomal protein L7A 38.3 62 0.0013 29.1 4.9 44 438-483 23-66 (104)
24 PF13155 Toprim_2: Toprim-like 34.7 1.4E+02 0.003 25.0 6.2 34 438-471 36-72 (96)
25 PF01408 GFO_IDH_MocA: Oxidore 34.2 2.4E+02 0.0051 24.1 7.7 36 440-477 54-89 (120)
26 cd03361 TOPRIM_TopoIA_RevGyr T 31.7 98 0.0021 29.9 5.4 28 431-460 103-130 (170)
27 COG0550 TopA Topoisomerase IA 30.8 75 0.0016 36.6 5.1 61 398-460 13-88 (570)
28 PF01248 Ribosomal_L7Ae: Ribos 29.9 1.1E+02 0.0024 25.9 4.9 44 438-483 21-65 (95)
29 COG0723 QcrA Rieske Fe-S prote 28.9 30 0.00065 33.1 1.4 21 206-226 114-135 (177)
30 cd08193 HVD 5-hydroxyvalerate 28.6 2.4E+02 0.0051 30.1 8.1 40 435-474 12-54 (376)
31 PF01751 Toprim: Toprim domain 27.9 96 0.0021 26.7 4.2 23 438-460 48-71 (100)
32 PRK09190 hypothetical protein; 27.7 1.7E+02 0.0038 29.8 6.6 46 438-483 117-166 (220)
33 PF05830 NodZ: Nodulation prot 27.3 42 0.00092 36.1 2.3 65 214-281 2-72 (321)
34 TIGR02195 heptsyl_trn_II lipop 27.0 3.1E+02 0.0067 28.1 8.4 57 405-470 173-229 (334)
35 smart00187 INB Integrin beta s 26.2 1.4E+02 0.003 33.5 6.0 53 411-471 260-313 (423)
36 cd08192 Fe-ADH7 Iron-containin 25.3 3.2E+02 0.0068 29.0 8.3 40 435-474 10-52 (370)
37 PF04123 DUF373: Domain of unk 25.3 1.3E+02 0.0028 32.8 5.4 61 433-494 83-145 (344)
38 cd06382 PBP1_iGluR_Kainate N-t 24.7 7E+02 0.015 25.1 10.3 95 430-543 110-207 (327)
39 COG0803 LraI ABC-type metal io 23.7 3.6E+02 0.0079 28.1 8.3 62 405-470 192-263 (303)
40 cd08182 HEPD Hydroxyethylphosp 23.4 3.4E+02 0.0074 28.8 8.1 38 435-472 9-46 (367)
41 TIGR01056 topB DNA topoisomera 23.3 1.1E+02 0.0024 35.6 4.9 28 433-460 80-107 (660)
42 PRK10017 colanic acid biosynth 22.9 2.6E+02 0.0056 30.9 7.3 63 405-471 233-304 (426)
43 PRK04175 rpl7ae 50S ribosomal 22.7 1.7E+02 0.0037 27.1 5.0 44 438-483 36-80 (122)
44 cd08551 Fe-ADH iron-containing 22.2 3.8E+02 0.0082 28.3 8.2 40 435-474 9-51 (370)
45 cd06355 PBP1_FmdD_like Peripla 21.6 8.1E+02 0.018 25.2 10.3 89 435-539 119-211 (348)
46 PF02186 TFIIE_beta: TFIIE bet 20.8 2E+02 0.0043 24.1 4.6 44 147-220 18-61 (65)
47 PF13728 TraF: F plasmid trans 20.0 1.4E+02 0.003 29.9 4.2 82 376-458 50-160 (215)
No 1
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.4e-84 Score=646.83 Aligned_cols=291 Identities=22% Similarity=0.380 Sum_probs=260.3
Q ss_pred CCCCccccccCCCCeEEEEEcCC--CCcccchhhhhhhhHHHHHhcCEEecCCCcccc----------ccceeeechhhh
Q 008526 201 IPNKRTVEWKPKSDKFLFAICLS--GQMSNHLICLEKHMFLAALLNRVLVIPSSKFDY----------QYSRVLDIEHIN 268 (563)
Q Consensus 201 ~~~~~~~~w~p~~gy~l~cpCmg--GnqanHflcleg~l~FAk~LNRTLVLPPw~i~Y----------~f~~fFDVesL~ 268 (563)
++.-+..+||| |||++|||||| |||||||| |+|+|||+||||||||| |++| ||+.||+||+|+
T Consensus 18 ~~~~~~~~~DP-~GYl~yCPCMGRFGNQaDhFL---GsLAFAKaLnRTL~lPp-wiEy~~pe~~n~~vpf~~yF~vepl~ 92 (386)
T KOG3849|consen 18 LPGMPAGSWDP-AGYLLYCPCMGRFGNQADHFL---GSLAFAKALNRTLVLPP-WIEYKHPETKNLMVPFEFYFQVEPLA 92 (386)
T ss_pred cCCCccCCCCC-CccEEEccccccccchHHHHH---HHHHHHHHhcccccCCc-chhccCCcccccccchhheeecccHh
Confidence 34556788999 69999999999 99999999 99999999999999999 8888 599999999999
Q ss_pred hhhCCcceeeHHHHHHHh-cCCCCC-Ce-eEEecC------CCCCCCCChHHHHHHhhhccCCCCcc-CCCCCCCCcCCC
Q 008526 269 DCLGRKVVVSFENFMEME-KNHAHI-DR-FLCYFG------LPQPCFVDDEHIKKLKQLGISMGKTE-TVWKNEDTRKPS 338 (563)
Q Consensus 269 ~y~~~~~VIemEeFmee~-~~~~pi-Dr-~yCY~~------~~~~C~~d~~~~~k~K~lG~~~Gnpf-pFWd~~~v~f~~ 338 (563)
+|| |||||+|||+++ +.+||. .| .|||.+ ++.+|+ +|+ |||| ||||+++|+|..
T Consensus 93 ~Yh---RVitm~dFm~klapthwp~~~Rva~c~k~a~qr~pdkp~Ch--------~Ke-----GNPFGPfWDqfhvsFv~ 156 (386)
T KOG3849|consen 93 KYH---RVITMQDFMKKLAPTHWPGTPRVAICDKSAAQRSPDKPGCH--------SKE-----GNPFGPFWDQFHVSFVG 156 (386)
T ss_pred hhh---hheeHHHHHHHhCcccCCCCcceeeeehhhhccCCCCCCCc--------ccC-----CCCCCCchhheEeeeec
Confidence 999 999999999994 555555 45 599987 788999 999 9999 999999999999
Q ss_pred cchhhhhhhccCCcchhhhhccccccchhhhcccC-----------CC----Cccccccc---ccccccHHHHHHHHHHH
Q 008526 339 KRTVQDIEGKFKTDDDVIAVGDLFYADVERDWVMQ-----------PG----GPINHRCK---TLIEPSRLIMVTAQRFV 400 (563)
Q Consensus 339 s~~~~~ll~kf~~~~~l~~Igd~F~~~~~~~W~~~-----------~G----~Pv~~k~r---kyL~wS~~I~~~A~~fI 400 (563)
+++++++- .|.-+...+++|.++ +| ||++.+++ |||+||++|+++|++||
T Consensus 157 sE~f~~i~------------Fd~~~~~~~~kW~~kfp~eeyPVLAf~gAPA~FPv~~e~~~lQkYl~WS~r~~e~~k~fI 224 (386)
T KOG3849|consen 157 SEYFGDIG------------FDLNQMGSRKKWLEKFPSEEYPVLAFSGAPAPFPVKGEVWSLQKYLRWSSRITEQAKKFI 224 (386)
T ss_pred cccccccc------------cchhhcchHHHHHhhCCcccCceeeecCCCCCCccccccccHHHHHHHHHHHHHHHHHHH
Confidence 99999664 344444456889877 45 66899887 99999999999999999
Q ss_pred HHhhCCCcEEeeeec-hhhhhhccCCC----------CC---------------CCCChHHHHHHHHHHHHHcC-CCEEE
Q 008526 401 QTFLGSNFIALHFRR-HGFLKFCNAKK----------PS---------------CFYPIPQAADCITRLAERAK-APVIY 453 (563)
Q Consensus 401 ~~aLggpYIgVHLRR-~DF~~ac~~~v----------Ps---------------C~psi~~aa~qI~~~vk~~~-lk~VF 453 (563)
+..|.+||||||||+ .||+++|++.+ || |.|+.++|.+||+++++.++ +++||
T Consensus 225 ~a~L~rpfvgiHLRng~DWvraCehikd~~~~hlfASpQClGy~~~~gaLt~e~C~Psk~~I~rqik~~v~si~dakSVf 304 (386)
T KOG3849|consen 225 SANLARPFVGIHLRNGADWVRACEHIKDTTNRHLFASPQCLGYGHHLGALTKEICSPSKQQILRQIKEKVGSIGDAKSVF 304 (386)
T ss_pred HHhcCcceeEEEeecCchHHHHHHHhcccCCCccccChhhccccccccccchhhhCccHHHHHHHHHHHHhhhcccceEE
Confidence 999999999999999 89999999832 44 99999999999999999996 99999
Q ss_pred EecCCChhhHHHHHHHHhhcCceeEEEeCCCCCCchhhhhHhhhccCCCchhHHHHHhHHHHhcCCccccccccccchHH
Q 008526 454 LSTDAAESETSLLQSLVVLNGKTIALVKRPPRNSAEKWDSLLYRHHLEDDSQVEAMLDKTICAMSNVFIGASGSTFTEDI 533 (563)
Q Consensus 454 IATDA~~~E~~eLk~lL~~~g~~v~vv~r~~~~~~e~~~~ll~kdg~~~Dg~vvAiIDq~Ica~A~~FIGtc~STFS~~I 533 (563)
||||. +++++||+.+|++ + .+.|++++| + ++.+|++|++|||||||||+||||+++
T Consensus 305 VAsDs-~hmi~Eln~aL~~-~-~i~vh~l~p--------------------d-d~y~dLaIlGqadhFiGNCvSsfsafv 360 (386)
T KOG3849|consen 305 VASDS-DHMIDELNEALKP-Y-EIEVHRLEP--------------------D-DMYTDLAILGQADHFIGNCVSSFSAFV 360 (386)
T ss_pred Eeccc-hhhhHHHHHhhcc-c-ceeEEecCc--------------------c-cchhhhhhhcccchhhhhhHHHHHHHH
Confidence 99999 8999999998874 4 466888775 3 577899999999999999999999999
Q ss_pred HHHHHhcCCCCCccc
Q 008526 534 MRLRKDWGSTSLCDE 548 (563)
Q Consensus 534 krERdl~G~pSsf~e 548 (563)
|||||..|+||.|.+
T Consensus 361 KRERD~~GrPS~FfG 375 (386)
T KOG3849|consen 361 KRERDHAGRPSAFFG 375 (386)
T ss_pred hhhhcccCCcchhcc
Confidence 999999999999987
No 2
>PF10250 O-FucT: GDP-fucose protein O-fucosyltransferase; InterPro: IPR019378 This is a family of conserved proteins representing the enzyme responsible for adding O-fucose to EGF (epidermal growth factor-like) repeats. Six highly conserved cysteines are present as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and Caenorhabditis elegans. Both features are characteristic of several glycosyltransferase families. The enzyme is a membrane-bound protein released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese []. ; PDB: 3ZY6_A 3ZY3_A 3ZY5_A 3ZY2_A 3ZY4_A.
Probab=100.00 E-value=3.2e-47 Score=381.50 Aligned_cols=290 Identities=26% Similarity=0.421 Sum_probs=166.4
Q ss_pred EEEEEcCC--CCcccchhhhhhhhHHHHHhcCEEecCCCccccc-----------cceeeechhhhhhhCCcceeeHHHH
Q 008526 216 FLFAICLS--GQMSNHLICLEKHMFLAALLNRVLVIPSSKFDYQ-----------YSRVLDIEHINDCLGRKVVVSFENF 282 (563)
Q Consensus 216 ~l~cpCmg--GnqanHflcleg~l~FAk~LNRTLVLPPw~i~Y~-----------f~~fFDVesL~~y~~~~~VIemEeF 282 (563)
++|||||| |||.++|. +.++||++||||||||||...|+ |+.|||+++|++++. +||+|+||
T Consensus 1 ~~y~p~~GGfnNQr~~~~---~a~~~A~~LnRTLVLPp~~~~~~~~~~~~~~~ipf~~~fD~~~l~~~~~--~vi~~~ef 75 (351)
T PF10250_consen 1 LVYDPCMGGFNNQRMGFE---NAVVFAKALNRTLVLPPFIKHYHWKDQSKQRHIPFSDFFDVEHLRKFLR--PVITMEEF 75 (351)
T ss_dssp EEE---SSSHHHHHHHHH---HHHHHHHHHT-EEE--EEEEESSSS----EEEEEHHHHB-HHHHTTTS----EE-HHHH
T ss_pred CccCCCCCCHHHHHHHHH---HHHHHHHHhCCEEEcCCccccccccccccccccChhhhccHHHHHHHhh--Cceehhee
Confidence 69999999 66666666 99999999999999999866563 888999999999984 89999999
Q ss_pred HHHhcCCCCCCe-eEEecCCCCCCCCChHHHHHHhhhccCCCCcc-CCCCCCCCcCCCcchh-h------h---hhhcc-
Q 008526 283 MEMEKNHAHIDR-FLCYFGLPQPCFVDDEHIKKLKQLGISMGKTE-TVWKNEDTRKPSKRTV-Q------D---IEGKF- 349 (563)
Q Consensus 283 mee~~~~~piDr-~yCY~~~~~~C~~d~~~~~k~K~lG~~~Gnpf-pFWd~~~v~f~~s~~~-~------~---ll~kf- 349 (563)
+.. .+....+ .+|+... .|..... .+|. |+++ ++|+...+.+...... . + ++.+.
T Consensus 76 ~~~--~~~~~~~~~~~~~~~--~~~~~~~---~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 143 (351)
T PF10250_consen 76 LPK--HWDEVFRLQYCWSPW--ESGSWDD---NMKD-----GNPFGPFWDKFPIKFDPCEFWSSPSLYLEDVLPELREWN 143 (351)
T ss_dssp HHH--HS-GGG-EEEESS-B-------------TTS-----STTHHHHHHHTT---SEEE-E-TTSTTTT-STTHHHHHH
T ss_pred ccc--hhccccchhhccccc--ccccchh---hccc-----cccccccccccceeeccccccCCchhhHHHhhhHHhhhc
Confidence 954 4454444 4776651 2221111 3455 7777 8888777665533311 1 0 00000
Q ss_pred -CCcchhhhhccccccchhhhcccCCCCcccccccccccccHHHHHHHHHHHHHhh--CCCcEEeeeech-hhhhhccCC
Q 008526 350 -KTDDDVIAVGDLFYADVERDWVMQPGGPINHRCKTLIEPSRLIMVTAQRFVQTFL--GSNFIALHFRRH-GFLKFCNAK 425 (563)
Q Consensus 350 -~~~~~l~~Igd~F~~~~~~~W~~~~G~Pv~~k~rkyL~wS~~I~~~A~~fI~~aL--ggpYIgVHLRR~-DF~~ac~~~ 425 (563)
.....++.+.. ....+..+.+ ...-+++|+|+..|.+.|++||+..+ ++||||||||+. ||.++|...
T Consensus 144 ~~~~~~~i~~~~-----~~~~~~~~~~---~~~~~r~l~~~~~i~~~a~~~i~~~~~~~~~yiavHlR~~~D~~~~C~~~ 215 (351)
T PF10250_consen 144 ENSEHPVIAFTG-----FESRLPDNYL---DRDLQRYLRFSPEIRELADKFIKRLLAGGGPYIAVHLRRGKDWFSACEFK 215 (351)
T ss_dssp HHTT-SEEEESS------SS-SS--GG---GGGGGGG--B-HHHHHHHHHHHHHH----SSEEEEEE--SHHHHHHHCT-
T ss_pred cccccccceecc-----ccccchhccc---CccceEEEecCHHHHHHHHHHHHHhhcccCceEEEeecccCchHhhcccC
Confidence 00001111100 0001110000 11124799999999999999999999 789999999996 999999961
Q ss_pred ---------------------C--CCCCCChHHHHHHHHHHHHHcCCCEEEEecCCCh---hhHHHHHHHHhhcCceeEE
Q 008526 426 ---------------------K--PSCFYPIPQAADCITRLAERAKAPVIYLSTDAAE---SETSLLQSLVVLNGKTIAL 479 (563)
Q Consensus 426 ---------------------v--PsC~psi~~aa~qI~~~vk~~~lk~VFIATDA~~---~E~~eLk~lL~~~g~~v~v 479 (563)
. ..|.|+.++++.+|++.+...+.++||||||... ..++.|++.++. .+
T Consensus 216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l~~~~~~---~~-- 290 (351)
T PF10250_consen 216 GERHLLASPRCWGKKSINPEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPLKNMFPN---VV-- 290 (351)
T ss_dssp T----TTTHHHH-GGGTT-----HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS-----------HHHHHH---HH--
T ss_pred CchHHHHHhHhhccccccchhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHHHHHhhh---hE--
Confidence 0 1288999999999999999999999999999943 355667777651 11
Q ss_pred EeCCCCCCchhhhhHhhhccCCCchhHHHHHhHHHHhcCCccccccccccchHHHHHHHhcCCCC
Q 008526 480 VKRPPRNSAEKWDSLLYRHHLEDDSQVEAMLDKTICAMSNVFIGASGSTFTEDIMRLRKDWGSTS 544 (563)
Q Consensus 480 v~r~~~~~~e~~~~ll~kdg~~~Dg~vvAiIDq~Ica~A~~FIGtc~STFS~~IkrERdl~G~pS 544 (563)
........+.++. +. ++. +|+|||+||++|++|||||+||||++|.++|...|+|.
T Consensus 291 -~~~~~~~~~~~~~--~~-----~~~-~a~vD~~i~~~s~~Figt~~Stfs~~i~~~R~~~g~~~ 346 (351)
T PF10250_consen 291 -TKDDLLSHEELEP--LN-----DDQ-LAMVDQEICSRSDVFIGTCGSTFSSNIARERHYRGKPK 346 (351)
T ss_dssp -GGGT--EE--S------------S---HHHHHHHHHHSSEEEE-TT-HHHHHHHHHHHHSSSS-
T ss_pred -eccccCCHHHhhh--cc-----ccc-hhHHHHHHHhcCCEEEecCcchhHHHhhcccCcCCCCC
Confidence 0110001111111 11 235 79999999999999999999999999999999999884
No 3
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=98.22 E-value=6e-06 Score=85.87 Aligned_cols=138 Identities=17% Similarity=0.221 Sum_probs=78.0
Q ss_pred ccccccHHHHHHHHHHHHHhhCC-CcEEeeeech---hhhhhccCCCCCCCCChHHHHHHHHHHHHHc------CCCEEE
Q 008526 384 TLIEPSRLIMVTAQRFVQTFLGS-NFIALHFRRH---GFLKFCNAKKPSCFYPIPQAADCITRLAERA------KAPVIY 453 (563)
Q Consensus 384 kyL~wS~~I~~~A~~fI~~aLgg-pYIgVHLRR~---DF~~ac~~~vPsC~psi~~aa~qI~~~vk~~------~lk~VF 453 (563)
..+++...|...-+.+.+.++.| +=||||.|.. |...- .|. +-..+.+.++|...+++. +-.+||
T Consensus 144 ~slkpR~eIqarID~iy~ehf~g~~~IGVHVRhGngeD~~~h----~~~-~~D~e~~L~~V~~ai~~ak~~~~~k~~~IF 218 (321)
T PF05830_consen 144 SSLKPRPEIQARIDAIYREHFAGYSVIGVHVRHGNGEDIMDH----APY-WADEERALRQVCTAIDKAKALAPPKPVRIF 218 (321)
T ss_dssp HHS-B-HHHHHHHHHHHHHHTTTSEEEEEEE--------------------HHHHHHHHHHHHHHHHHHTS--SS-EEEE
T ss_pred HhCCCCHHHHHHHHHHHHHHcCCCceEEEEEeccCCcchhcc----Ccc-ccCchHHHHHHHHHHHHHHhccCCCCeeEE
Confidence 78999999999999999988765 6999999973 22211 111 001222344444433332 345699
Q ss_pred EecCCChhhHHHHHHHHhhcCceeEEEeCCCCCCchhhhhHhhhccCCCchhHHHHHhHHHHhcCCccc-cccccccchH
Q 008526 454 LSTDAAESETSLLQSLVVLNGKTIALVKRPPRNSAEKWDSLLYRHHLEDDSQVEAMLDKTICAMSNVFI-GASGSTFTED 532 (563)
Q Consensus 454 IATDA~~~E~~eLk~lL~~~g~~v~vv~r~~~~~~e~~~~ll~kdg~~~Dg~vvAiIDq~Ica~A~~FI-Gtc~STFS~~ 532 (563)
||||. ...++++++.|+ + ++++.+.++....-.++. ...| -+|+..|+||.+.||+.|+.| =+.-|+||-.
T Consensus 219 LATDS-aeVid~fr~~FP--d-iiti~k~F~~~~~g~Lhs--~~~g--~~gg~~ALIDM~LLSrCD~LIr~~ptS~Fsr~ 290 (321)
T PF05830_consen 219 LATDS-AEVIDQFRKKFP--D-IITIPKQFPASQAGPLHS--AAVG--IEGGESALIDMYLLSRCDYLIRFPPTSAFSRY 290 (321)
T ss_dssp EEES--HHHHHHHHHHST--T-EE------------------HHHH--HHHHHHHHHHHHHHTTSSEEEEESTT-GGGHH
T ss_pred EecCc-HHHHHHHHHHCC--C-eEEcccccCCCCCCcCcc--cccc--cchHHHHHHHHHHHHhCCeEEEcCCCchhhhH
Confidence 99999 678999999997 4 454545443221111221 1111 245668999999999999999 6999999965
Q ss_pred HH
Q 008526 533 IM 534 (563)
Q Consensus 533 Ik 534 (563)
-.
T Consensus 291 as 292 (321)
T PF05830_consen 291 AS 292 (321)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 4
>PF01531 Glyco_transf_11: Glycosyl transferase family 11; InterPro: IPR002516 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 11 GT11 from CAZY comprises enzymes with only one known activity; galactoside 2-L-fucosyltransferase (2.4.1.69 from EC). Some of the proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Galactoside 2-L-fucosyltransferase 1 (2.4.1.69 from EC) and Galactoside 2-L-fucosyltransferase 2 (2.4.1.69 from EC) belong to the Hh blood group system and are associated with H/h and Se/se antigens.; GO: 0008107 galactoside 2-alpha-L-fucosyltransferase activity, 0005975 carbohydrate metabolic process, 0016020 membrane
Probab=97.94 E-value=7.4e-05 Score=76.20 Aligned_cols=103 Identities=18% Similarity=0.252 Sum_probs=67.8
Q ss_pred CCCcEEeeeechhhhhhccCC--CCCCCCChHHHHHHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCceeEEEeC
Q 008526 405 GSNFIALHFRRHGFLKFCNAK--KPSCFYPIPQAADCITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGKTIALVKR 482 (563)
Q Consensus 405 ggpYIgVHLRR~DF~~ac~~~--vPsC~psi~~aa~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v~vv~r 482 (563)
..+.||||.||.||+..-... -+.| +.+=..+.|..+.++..-.++||.||.. +-.++.+......+ ++ .
T Consensus 162 ~~~~V~VHIRRGDy~~~~~~~~~~~~~--~~~Yy~~Ai~~i~~~~~~~~f~ifSDD~----~w~k~~l~~~~~~~-~~-~ 233 (298)
T PF01531_consen 162 NSNSVCVHIRRGDYVSNGNHNWKHGIC--DKDYYKKAIEYIREKVKNPKFFIFSDDI----EWCKENLKFSNGDV-YF-S 233 (298)
T ss_pred CCCeEEEEEEchhccccccccccCCCC--CHHHHHHHHHHHHHhCCCCEEEEEcCCH----HHHHHHHhhcCCcE-EE-E
Confidence 458999999999998765441 1222 2444455666666666778899999983 34444443111111 11 1
Q ss_pred CCCCCchhhhhHhhhccCCCchhHHHHHhHHHHhcCCccccccccccchHHHHHH
Q 008526 483 PPRNSAEKWDSLLYRHHLEDDSQVEAMLDKTICAMSNVFIGASGSTFTEDIMRLR 537 (563)
Q Consensus 483 ~~~~~~e~~~~ll~kdg~~~Dg~vvAiIDq~Ica~A~~FIGtc~STFS~~IkrER 537 (563)
. + . .+..|.+.+++++|+|++. ||||--....-
T Consensus 234 ~-------------------~-~-~~~~Dl~lms~C~~~Iisn-STFswW~a~L~ 266 (298)
T PF01531_consen 234 G-------------------N-N-SPYEDLYLMSQCKHFIISN-STFSWWAAYLS 266 (298)
T ss_pred C-------------------C-C-CHHHHHHHHHhCCcEEECC-ChHHHHHHHHC
Confidence 0 0 2 4777999999999999995 99998887664
No 5
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=92.58 E-value=0.17 Score=55.38 Aligned_cols=132 Identities=15% Similarity=0.159 Sum_probs=73.2
Q ss_pred CCCcEEeeeechhhhhhccCCCCCCCCChHHHHHHHHHHH---HH---cCCCEEEEecCCChhhHHHHHHHHhhcCceeE
Q 008526 405 GSNFIALHFRRHGFLKFCNAKKPSCFYPIPQAADCITRLA---ER---AKAPVIYLSTDAAESETSLLQSLVVLNGKTIA 478 (563)
Q Consensus 405 ggpYIgVHLRR~DF~~ac~~~vPsC~psi~~aa~qI~~~v---k~---~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v~ 478 (563)
.+|-||||.||.|=+-.-. -|-++++-...+..+- ++ .-.+.||+|||- ..-++|-+.--+ +++
T Consensus 361 ~~PivGvhvRRTDKVGTEA-----AfH~~eEYM~~vE~~f~~le~rg~~~~rRiflAsDD-p~vv~EAk~kYP-nYe--- 430 (580)
T KOG3705|consen 361 DKPIVGVHVRRTDKVGTEA-----AFHALEEYMEWVEIWFKVLEKRGKPLERRIFLASDD-PTVVPEAKNKYP-NYE--- 430 (580)
T ss_pred CCceeeEEEEecccccchh-----hhhhHHHHHHHHHHHHHHHHHhCCchhheEEEecCC-chhchHhhccCC-CcE---
Confidence 3599999999987432111 1222555444333322 22 237889999998 556666555443 232
Q ss_pred EEeCCCCCCchhhhhH---hhhccCCCchhHHHHHhHHHHhcCCccccccccccchHHHHHHHhcC------CCCCcccc
Q 008526 479 LVKRPPRNSAEKWDSL---LYRHHLEDDSQVEAMLDKTICAMSNVFIGASGSTFTEDIMRLRKDWG------STSLCDEY 549 (563)
Q Consensus 479 vv~r~~~~~~e~~~~l---l~kdg~~~Dg~vvAiIDq~Ica~A~~FIGtc~STFS~~IkrERdl~G------~pSsf~e~ 549 (563)
++.-+ .-.|.+- .|-|..+ .| -|+|-.|++++||.+.|..|..---.+|-+.-+| |-|-=|-|
T Consensus 431 ~igd~----eia~~A~l~nRYTd~sL--~G--vIlDIh~LS~~d~LVCTFSSQVCRvaYEimQt~~pDa~~~FhSLDDIY 502 (580)
T KOG3705|consen 431 VIGDT----EIAKTAQLNNRYTDASL--MG--VILDIHILSKVDYLVCTFSSQVCRVAYEIMQTSGPDAGSKFHSLDDIY 502 (580)
T ss_pred EeccH----HHHHHhhccccchhhhh--hh--eeeeeeeecccceEEEechHHHHHHHHHHHhccCCCccccccccccee
Confidence 22221 1123332 2433211 14 3789999999999998755555545555565554 33433556
Q ss_pred ccCCC
Q 008526 550 LCQGE 554 (563)
Q Consensus 550 ~c~~~ 554 (563)
.-+|.
T Consensus 503 YfGGQ 507 (580)
T KOG3705|consen 503 YFGGQ 507 (580)
T ss_pred eecCc
Confidence 55554
No 6
>PF03254 XG_FTase: Xyloglucan fucosyltransferase; InterPro: IPR004938 Plant cell walls are crucial for development, signal transduction, and disease resistance in plants. Cell walls are made of cellulose, hemicelluloses, and pectins. Xyloglucan (XG), the principal load-bearing hemicellulose of dicotyledonous plants, has a terminal fucosyl residue. This fucosyltransferase adds this residue []. ; GO: 0008107 galactoside 2-alpha-L-fucosyltransferase activity, 0042546 cell wall biogenesis, 0016020 membrane
Probab=90.90 E-value=3 Score=46.68 Aligned_cols=139 Identities=17% Similarity=0.223 Sum_probs=93.4
Q ss_pred cccccccHHHHHHHHHHHHHhhCC--CcEEeeeechhhhhhccCCCCCCCCChHHHHHHHHHH-----------------
Q 008526 383 KTLIEPSRLIMVTAQRFVQTFLGS--NFIALHFRRHGFLKFCNAKKPSCFYPIPQAADCITRL----------------- 443 (563)
Q Consensus 383 rkyL~wS~~I~~~A~~fI~~aLgg--pYIgVHLRR~DF~~ac~~~vPsC~psi~~aa~qI~~~----------------- 443 (563)
|-++.|++.+=....+|=+..|-+ -=|||-.|.-++... |. ..-.++|..|+++-
T Consensus 275 RYLfhPsN~VW~~Itryy~ayLa~Ad~riGIQIRvf~~~~~-----~~-~~~~dqIl~C~~~e~LLP~v~~~~~~~~~~~ 348 (476)
T PF03254_consen 275 RYLFHPSNQVWGLITRYYDAYLAKADERIGIQIRVFDPKPG-----PF-QHVLDQILSCTQQEKLLPEVVDTQEPAASSS 348 (476)
T ss_pred HHHcCCCchhHHHHHHHHHHHccCcCceeEEEEEecCCCCC-----cc-hhHHHHHHHHHhhcccCCCcccccccccccc
Confidence 356778888877888887777765 369999999665331 11 00144444444332
Q ss_pred HHHcCCCEEEEecCCChhhHHHHHHHHhh----cCceeEEEeCCCCCCchhhhhHhhhccCCCchhHHHHHhHHHHhcCC
Q 008526 444 AERAKAPVIYLSTDAAESETSLLQSLVVL----NGKTIALVKRPPRNSAEKWDSLLYRHHLEDDSQVEAMLDKTICAMSN 519 (563)
Q Consensus 444 vk~~~lk~VFIATDA~~~E~~eLk~lL~~----~g~~v~vv~r~~~~~~e~~~~ll~kdg~~~Dg~vvAiIDq~Ica~A~ 519 (563)
.+..+.+.|+|++.. ..+.+.|+.+.-. .|++| -|..+++++.+.+ |....++ -|.+|-|+++.+|
T Consensus 349 ~~~~~~kaVlVtSL~-~~yye~lr~~Y~~~~t~tGe~V-~V~QpShe~~Q~~-------~~~~h~~-kAlaEmyLLS~sD 418 (476)
T PF03254_consen 349 SKSQKSKAVLVTSLY-SEYYEKLRNMYWEHPTVTGEVV-GVHQPSHEEYQQF-------GDNMHNQ-KALAEMYLLSLSD 418 (476)
T ss_pred CCCCceEEEEEEeCC-HHHHHHHHHHHhcCCCcCCcEE-EEECCCCcccccc-------cccchHH-HHHHHHHHHHhcc
Confidence 112357889999999 5678889988742 24444 5566776554432 2223345 7999999999999
Q ss_pred ccccccccccchHHHHHH
Q 008526 520 VFIGASGSTFTEDIMRLR 537 (563)
Q Consensus 520 ~FIGtc~STFS~~IkrER 537 (563)
..|-|.-|||-+--+-..
T Consensus 419 ~LVTS~~STFGYVAqgLg 436 (476)
T PF03254_consen 419 VLVTSGWSTFGYVAQGLG 436 (476)
T ss_pred ceEecCCCCchhHHHhhc
Confidence 999999999998877443
No 7
>PRK07283 hypothetical protein; Provisional
Probab=74.59 E-value=12 Score=32.97 Aligned_cols=44 Identities=11% Similarity=0.159 Sum_probs=33.7
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCceeEEEeCC
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGKTIALVKRP 483 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v~vv~r~ 483 (563)
+++.+.+++-+++-||+|+|+++...+.+.+.-. ...||++..+
T Consensus 24 ~~v~~aik~gk~~lVi~A~Das~~~~kk~~~~~~--~~~Vp~~~~~ 67 (98)
T PRK07283 24 ELVVKAIQSGQAKLVFLANDAGPNLTKKVTDKSN--YYQVEVSTVF 67 (98)
T ss_pred HHHHHHHHcCCccEEEEeCCCCHHHHHHHHHHHH--HcCCCEEEeC
Confidence 5677777777899999999999888888887754 2456666554
No 8
>PRK06683 hypothetical protein; Provisional
Probab=70.62 E-value=8.8 Score=33.15 Aligned_cols=44 Identities=11% Similarity=0.102 Sum_probs=33.6
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCceeEEEeCC
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGKTIALVKRP 483 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v~vv~r~ 483 (563)
++..+.+++-+++-||||.|+++.-.+.+..+=. ...||++..+
T Consensus 17 ~~v~kaik~gkaklViiA~Da~~~~~~~i~~~~~--~~~Vpv~~~~ 60 (82)
T PRK06683 17 KRTLEAIKNGIVKEVVIAEDADMRLTHVIIRTAL--QHNIPITKVE 60 (82)
T ss_pred HHHHHHHHcCCeeEEEEECCCCHHHHHHHHHHHH--hcCCCEEEEC
Confidence 5666667778899999999998887777777665 3567776655
No 9
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=66.24 E-value=13 Score=32.32 Aligned_cols=44 Identities=20% Similarity=0.258 Sum_probs=33.0
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCceeEEEeCC
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGKTIALVKRP 483 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v~vv~r~ 483 (563)
+++.+.+++-+++-||||+|+++.-.+.|..+=. ...||++..+
T Consensus 14 ~~vlkaIk~gkakLViiA~Da~~~~~k~i~~~c~--~~~Vpv~~~~ 57 (82)
T PRK13601 14 KQTLKAITNCNVLQVYIAKDAEEHVTKKIKELCE--EKSIKIVYID 57 (82)
T ss_pred HHHHHHHHcCCeeEEEEeCCCCHHHHHHHHHHHH--hCCCCEEEeC
Confidence 5666667777899999999998877777777665 3557775544
No 10
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=64.21 E-value=15 Score=32.30 Aligned_cols=45 Identities=9% Similarity=0.045 Sum_probs=35.2
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCceeEEEeCCC
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGKTIALVKRPP 484 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v~vv~r~~ 484 (563)
+|..+.+++-.++.||||-|++...+..|..+-. .+.+|+++-++
T Consensus 19 kqt~Kai~kg~~~~v~iA~Da~~~vv~~l~~lce--ek~Ip~v~V~s 63 (84)
T PRK13600 19 KETLKALKKDQVTSLIIAEDVEVYLMTRVLSQIN--QKNIPVSFFKS 63 (84)
T ss_pred HHHHHHHhcCCceEEEEeCCCCHHHHHHHHHHHH--HcCCCEEEECC
Confidence 6667777777899999999998887777777776 45677777664
No 11
>COG2879 Uncharacterized small protein [Function unknown]
Probab=63.85 E-value=3.1 Score=35.10 Aligned_cols=26 Identities=23% Similarity=0.465 Sum_probs=24.6
Q ss_pred cceeeechhhhhhhCCcceeeHHHHHHH
Q 008526 258 YSRVLDIEHINDCLGRKVVVSFENFMEM 285 (563)
Q Consensus 258 f~~fFDVesL~~y~~~~~VIemEeFmee 285 (563)
|++| ||+++.-|.++||.|.|||..+
T Consensus 25 YdnY--Vehmr~~hPd~p~mT~~EFfre 50 (65)
T COG2879 25 YDNY--VEHMRKKHPDKPPMTYEEFFRE 50 (65)
T ss_pred HHHH--HHHHHHhCcCCCcccHHHHHHH
Confidence 6888 9999999999999999999988
No 12
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=58.60 E-value=19 Score=30.95 Aligned_cols=44 Identities=16% Similarity=0.177 Sum_probs=32.6
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCceeEEEeCC
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGKTIALVKRP 483 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v~vv~r~ 483 (563)
+++.+.+++-+++-||||.|+++.....+..+=. ...||++..+
T Consensus 17 ~~v~kai~~gkaklViiA~D~~~~~~~~i~~~c~--~~~Vp~~~~~ 60 (82)
T PRK13602 17 KQTVKALKRGSVKEVVVAEDADPRLTEKVEALAN--EKGVPVSKVD 60 (82)
T ss_pred HHHHHHHHcCCeeEEEEECCCCHHHHHHHHHHHH--HcCCCEEEEC
Confidence 5666667777899999999998877777766665 3457776655
No 13
>PRK09375 quinolinate synthetase; Provisional
Probab=53.30 E-value=64 Score=34.66 Aligned_cols=107 Identities=13% Similarity=0.119 Sum_probs=57.3
Q ss_pred cchhhhhhhccCCcchhhhhccccccchhhhcccC-----CC-CcccccccccccccHHHHHHHHHHHHHhhCCCcEEee
Q 008526 339 KRTVQDIEGKFKTDDDVIAVGDLFYADVERDWVMQ-----PG-GPINHRCKTLIEPSRLIMVTAQRFVQTFLGSNFIALH 412 (563)
Q Consensus 339 s~~~~~ll~kf~~~~~l~~Igd~F~~~~~~~W~~~-----~G-~Pv~~k~rkyL~wS~~I~~~A~~fI~~aLggpYIgVH 412 (563)
|+..-.+....+.++.++++||.|-+......+.+ .| =|+.+... ..-+.+ .+..-++..|-+|
T Consensus 144 SSnAl~iv~~~~~~~~IlF~PD~~Lg~~v~~l~~k~vilw~G~C~vH~~~~------~e~i~~----~r~~~Pda~Vv~H 213 (319)
T PRK09375 144 SSNAVKIVEALPQGKKILFLPDQHLGRYVAKQTGADIILWPGHCIVHEEFT------AEDLER----LRAEYPDAKVLVH 213 (319)
T ss_pred CHHHHHHHhccCCCCeEEEeCchHHHHHHHHcCCCEEEccCCcchhccCcC------HHHHHH----HHHHCcCCeEEEe
Confidence 43333455566667889999999976544332211 01 11111111 111111 1222244444455
Q ss_pred eechhhhhhccCCCCCCCCChHHHH------HHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHh
Q 008526 413 FRRHGFLKFCNAKKPSCFYPIPQAA------DCITRLAERAKAPVIYLSTDAAESETSLLQSLVV 471 (563)
Q Consensus 413 LRR~DF~~ac~~~vPsC~psi~~aa------~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~ 471 (563)
|-|-+.+..++ ..+.+.++....+.+.|+||. .....|++..+
T Consensus 214 --------------PEc~~eV~a~AD~vgSTs~~i~~v~~~~~~~~iigTE~--~L~~~l~~~~P 262 (319)
T PRK09375 214 --------------PECPPEVVALADFVGSTSQIIKAAKASPAKKFIVGTEI--GIVHRLQKANP 262 (319)
T ss_pred --------------cCCCHHHHHhcCEEecHHHHHHHHHhCCCCeEEEEccH--HHHHHHHHHCC
Confidence 44544444443 455666677778999999998 36777777765
No 14
>PRK07714 hypothetical protein; Provisional
Probab=50.10 E-value=39 Score=29.78 Aligned_cols=44 Identities=18% Similarity=0.212 Sum_probs=33.2
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCceeEEEeCC
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGKTIALVKRP 483 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v~vv~r~ 483 (563)
+++.+.+++-+++-|++|+|+++...+.+..+=. ...+|++..+
T Consensus 24 ~~v~~al~~g~~~lViiA~D~s~~~~~ki~~~~~--~~~vp~~~~~ 67 (100)
T PRK07714 24 ELVLKEVRSGKAKLVLLSEDASVNTTKKITDKCT--YYNVPMRKVE 67 (100)
T ss_pred HHHHHHHHhCCceEEEEeCCCCHHHHHHHHHHHH--hcCCCEEEeC
Confidence 5667777777899999999999888888887644 2346666544
No 15
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=47.17 E-value=34 Score=31.07 Aligned_cols=42 Identities=10% Similarity=0.126 Sum_probs=31.9
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCceeEEEe
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGKTIALVK 481 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v~vv~ 481 (563)
+++.+.+++-+++-||||+|+++...+.++.+=. ...||++.
T Consensus 31 ~~vlkalk~gkaklViiA~D~~~~~kkki~~~~~--~~~Vpv~~ 72 (108)
T PTZ00106 31 KSTLKALRNGKAKLVIISNNCPPIRRSEIEYYAM--LSKTGVHH 72 (108)
T ss_pred HHHHHHHHcCCeeEEEEeCCCCHHHHHHHHHHHh--hcCCCEEE
Confidence 5566666777899999999998888888887765 24466654
No 16
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=47.15 E-value=38 Score=30.05 Aligned_cols=43 Identities=7% Similarity=0.074 Sum_probs=31.4
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCceeEEEeC
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGKTIALVKR 482 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v~vv~r 482 (563)
+++.+.+++-+++-||||+|+++...+.+..+=. ...+|++..
T Consensus 22 ~~v~kai~~gkaklViiA~D~~~~~~~~i~~~c~--~~~Ip~~~~ 64 (99)
T PRK01018 22 KRTIKAIKLGKAKLVIVASNCPKDIKEDIEYYAK--LSGIPVYEY 64 (99)
T ss_pred HHHHHHHHcCCceEEEEeCCCCHHHHHHHHHHHH--HcCCCEEEE
Confidence 4556666777899999999998877777777755 245666443
No 17
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general b
Probab=42.74 E-value=28 Score=32.10 Aligned_cols=26 Identities=27% Similarity=0.382 Sum_probs=21.1
Q ss_pred hHHHHHHHHHHHHHcCCCEEEEecCCCh
Q 008526 433 IPQAADCITRLAERAKAPVIYLSTDAAE 460 (563)
Q Consensus 433 i~~aa~qI~~~vk~~~lk~VFIATDA~~ 460 (563)
.....+.|++++++ ++.|++|||++.
T Consensus 77 ~~~~~~~ik~l~~~--~d~iiiAtD~Dr 102 (142)
T cd01028 77 KKKQLKALKKLAKK--ADEIVLATDPDR 102 (142)
T ss_pred HHHHHHHHHHHHhc--CCEEEEcCCCCc
Confidence 66677888888865 699999999954
No 18
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=41.26 E-value=63 Score=30.55 Aligned_cols=49 Identities=14% Similarity=0.266 Sum_probs=35.7
Q ss_pred CcEEeeeechhhhhhccCCCCCCCCChHHHHHHHHHHHHHc--CCCEEEEecCCChhhHHHHHHHH
Q 008526 407 NFIALHFRRHGFLKFCNAKKPSCFYPIPQAADCITRLAERA--KAPVIYLSTDAAESETSLLQSLV 470 (563)
Q Consensus 407 pYIgVHLRR~DF~~ac~~~vPsC~psi~~aa~qI~~~vk~~--~lk~VFIATDA~~~E~~eLk~lL 470 (563)
.||||.+.- + . . . .+++.++|.+.+++. ++..|||+||.. .+.+|+++=
T Consensus 102 a~Vav~~~~-~--~---~---~----~~~i~~~V~~~v~~~~p~~~~V~Vs~D~~--~~~ri~~~~ 152 (177)
T PF09580_consen 102 AYVAVDLDF-N--R---F---N----TKKIKKKVEKAVKSADPRIYNVYVSTDPD--IFDRIRNLA 152 (177)
T ss_pred EEEEEEecc-c--c---c---c----hhHHHHHHHHHHHHhCCCccEEEEEcCHH--HHHHHHHHH
Confidence 899999993 2 1 1 1 567899999999995 458999999993 455555543
No 19
>TIGR03609 S_layer_CsaB polysaccharide pyruvyl transferase CsaB. The CsaB protein (cell surface anchoring B) of Bacillus anthracis adds a pyruvoyl group to peptidoglycan-associated polysaccharide. This addition is required for proteins with an S-layer homology domain (pfam00395) to bind. Within the larger group of proteins described by Pfam model pfam04230, this model represents a distinct clade that nearly exactly follows the phylogenetic distribution of the S-layer homology domain (pfam00395).
Probab=41.04 E-value=1.3e+02 Score=30.46 Aligned_cols=58 Identities=14% Similarity=0.186 Sum_probs=38.2
Q ss_pred CCCcEEeeeechhhhhhccCCCCCCCCChHHHHHHHHHHHHHcCCCEEEEecCCC--hhhHHHHHHHHh
Q 008526 405 GSNFIALHFRRHGFLKFCNAKKPSCFYPIPQAADCITRLAERAKAPVIYLSTDAA--ESETSLLQSLVV 471 (563)
Q Consensus 405 ggpYIgVHLRR~DF~~ac~~~vPsC~psi~~aa~qI~~~vk~~~lk~VFIATDA~--~~E~~eLk~lL~ 471 (563)
.+++|++.+|. |.. .+... ++.+++.|..+.++.+.+.++|+.... ....++|.+.+.
T Consensus 171 ~~~~i~i~~r~--~~~---~~~~~----~~~l~~~l~~l~~~~g~~v~~i~~~~~~D~~~~~~l~~~~~ 230 (298)
T TIGR03609 171 PEPVIVVSLRP--WPL---LDVSR----LLRLLRALDRLQRDTGAFVLFLPFQQPQDLPLARALRDQLL 230 (298)
T ss_pred CCCeEEEEECC--CCc---CCHHH----HHHHHHHHHHHHHhhCCeEEEEeCCcchhHHHHHHHHHhcC
Confidence 35899999986 211 01111 567888899999999999999997642 233455666553
No 20
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=39.83 E-value=34 Score=31.95 Aligned_cols=26 Identities=31% Similarity=0.399 Sum_probs=21.5
Q ss_pred hHHHHHHHHHHHHHcCCCEEEEecCCCh
Q 008526 433 IPQAADCITRLAERAKAPVIYLSTDAAE 460 (563)
Q Consensus 433 i~~aa~qI~~~vk~~~lk~VFIATDA~~ 460 (563)
.+...+.|++++++ ++.|++|||++.
T Consensus 85 ~~~~~~~ik~l~~~--ad~ii~atD~Dr 110 (151)
T cd03362 85 KKKQFKVLKKLAKR--ADEIVIATDADR 110 (151)
T ss_pred HHHHHHHHHHHHhC--CCeEEEccCCCc
Confidence 66677888888875 699999999954
No 21
>TIGR02201 heptsyl_trn_III lipopolysaccharide heptosyltransferase III, putative. This family consists of examples of the putative ADP-heptose:LPS heptosyltransferase III, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria. This enzyme may be less widely distributed than heptosyltransferases I and II.
Probab=38.88 E-value=1.8e+02 Score=29.92 Aligned_cols=58 Identities=14% Similarity=0.103 Sum_probs=33.0
Q ss_pred cHHHHHHHHHHHHHh-hCCCcEEeeeechhhhhhccCCCCCCCCChHHHHHHHHHHHHHcCCCEEEEec
Q 008526 389 SRLIMVTAQRFVQTF-LGSNFIALHFRRHGFLKFCNAKKPSCFYPIPQAADCITRLAERAKAPVIYLST 456 (563)
Q Consensus 389 S~~I~~~A~~fI~~a-LggpYIgVHLRR~DF~~ac~~~vPsC~psi~~aa~qI~~~vk~~~lk~VFIAT 456 (563)
+..-...++.++... .+++||++|-=- ..|.-..|.+.-++-++.+.++ +.+.|++.+
T Consensus 163 ~~~~~~~~~~~l~~~~~~~~~i~i~p~a---------~~~~K~Wp~e~~~~l~~~l~~~-~~~ivl~g~ 221 (344)
T TIGR02201 163 PPADWKAMRALLDEAGVGQNYIVIQPTS---------RWFFKCWDNDRFSALIDALHAR-GYEVVLTSG 221 (344)
T ss_pred CHHHHHHHHHHHHhcCCCCCEEEEeCCC---------CccccCCCHHHHHHHHHHHHhC-CCeEEEecC
Confidence 333344556666554 467999999421 1123334466666555555544 788887765
No 22
>PF02348 CTP_transf_3: Cytidylyltransferase; InterPro: IPR003329 Synonym(s): CMP-N-acetylneuraminic acid synthetase Acylneuraminate cytidylyltransferase (2.7.7.43 from EC) (CMP-NeuAc synthetase) catalyzes the reaction of CTP and NeuAc to form CMP-NeuAc, which is the nucleotide sugar donor used by sialyltransferases []. The outer membrane lipooligosaccharides of some microorganisms contain terminal sialic acid attached to N-acetyllactosamine and so this modification may be important in pathogenesis.; GO: 0009103 lipopolysaccharide biosynthetic process; PDB: 3K8D_C 1VH1_B 3K8E_C 1QWJ_A 3EWI_A 1VIC_B 3DUV_A 1VH3_C 3TQD_A 2Y6P_C ....
Probab=38.60 E-value=1.3e+02 Score=28.49 Aligned_cols=24 Identities=21% Similarity=0.142 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCC
Q 008526 435 QAADCITRLAERAKAPVIYLSTDA 458 (563)
Q Consensus 435 ~aa~qI~~~vk~~~lk~VFIATDA 458 (563)
.+...|.++.+--.++.|+||||.
T Consensus 26 Li~~~i~~a~~s~~~d~IvVaTd~ 49 (217)
T PF02348_consen 26 LIEYVIERAKQSKLIDEIVVATDD 49 (217)
T ss_dssp HHHHHHHHHHHTTTTSEEEEEESS
T ss_pred HHHHHHHHHHhCCCCCeEEEeCCC
Confidence 366667666666678999999999
No 23
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=38.27 E-value=62 Score=29.12 Aligned_cols=44 Identities=14% Similarity=0.180 Sum_probs=33.3
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCceeEEEeCC
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGKTIALVKRP 483 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v~vv~r~ 483 (563)
+++.+.+++-+++-|++|+|+.+...+.++.+-. ...||++...
T Consensus 23 ~~v~~aik~gk~~lVI~A~D~s~~~kkki~~~~~--~~~vp~~~~~ 66 (104)
T PRK05583 23 NKCEEAIKKKKVYLIIISNDISENSKNKFKNYCN--KYNIPYIEGY 66 (104)
T ss_pred HHHHHHHHcCCceEEEEeCCCCHhHHHHHHHHHH--HcCCCEEEec
Confidence 4566667777899999999999988998888754 2456665544
No 24
>PF13155 Toprim_2: Toprim-like
Probab=34.67 E-value=1.4e+02 Score=25.03 Aligned_cols=34 Identities=18% Similarity=0.127 Sum_probs=26.1
Q ss_pred HHHHHHHHHcCCCEEEEecCCChh---hHHHHHHHHh
Q 008526 438 DCITRLAERAKAPVIYLSTDAAES---ETSLLQSLVV 471 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~---E~~eLk~lL~ 471 (563)
+++.+.+++.+.+.|++|.|+++. ..+.+++.+.
T Consensus 36 ~~~~~~l~~~~~~~i~l~~DnD~aG~~~~~~~~~~l~ 72 (96)
T PF13155_consen 36 KQQIKFLKENPYKKIVLAFDNDEAGRKAAEKLQKELK 72 (96)
T ss_pred HHHHHHHHhCCCCcEEEEeCCCHHHHHHHHHHHHHHH
Confidence 577788877667999999999874 4666666665
No 25
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=34.22 E-value=2.4e+02 Score=24.15 Aligned_cols=36 Identities=14% Similarity=0.288 Sum_probs=27.9
Q ss_pred HHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCcee
Q 008526 440 ITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGKTI 477 (563)
Q Consensus 440 I~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~~v 477 (563)
+..++...+++.|+|||.. ....+..++++.. |+.|
T Consensus 54 ~~~ll~~~~~D~V~I~tp~-~~h~~~~~~~l~~-g~~v 89 (120)
T PF01408_consen 54 LEELLADEDVDAVIIATPP-SSHAEIAKKALEA-GKHV 89 (120)
T ss_dssp HHHHHHHTTESEEEEESSG-GGHHHHHHHHHHT-TSEE
T ss_pred HHHHHHhhcCCEEEEecCC-cchHHHHHHHHHc-CCEE
Confidence 4555666689999999999 7788888889874 6544
No 26
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=31.67 E-value=98 Score=29.88 Aligned_cols=28 Identities=14% Similarity=0.190 Sum_probs=21.7
Q ss_pred CChHHHHHHHHHHHHHcCCCEEEEecCCCh
Q 008526 431 YPIPQAADCITRLAERAKAPVIYLSTDAAE 460 (563)
Q Consensus 431 psi~~aa~qI~~~vk~~~lk~VFIATDA~~ 460 (563)
++.+.+.+.|+++++ +++.|++|||++.
T Consensus 103 ~~~~~~~~~l~~l~~--~~~~iiiatD~dr 130 (170)
T cd03361 103 DDKLETLEALRELAL--EVDEVLIATDPDT 130 (170)
T ss_pred cchHHHHHHHHHHHh--hCCEEEEecCCCc
Confidence 346677788888885 4789999999954
No 27
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=30.83 E-value=75 Score=36.59 Aligned_cols=61 Identities=23% Similarity=0.431 Sum_probs=34.6
Q ss_pred HHHHHhhCCCcEEe----eeechhhh----hhccCCCC----C--CCCC-hHHHHHHHHHHHHHcCCCEEEEecCCCh
Q 008526 398 RFVQTFLGSNFIAL----HFRRHGFL----KFCNAKKP----S--CFYP-IPQAADCITRLAERAKAPVIYLSTDAAE 460 (563)
Q Consensus 398 ~fI~~aLggpYIgV----HLRR~DF~----~ac~~~vP----s--C~ps-i~~aa~qI~~~vk~~~lk~VFIATDA~~ 460 (563)
+=|...||++|+-+ |+|--++- ..-..+.| . -.+. .+.++..|+.+++ +++.||||||.+.
T Consensus 13 k~Ia~~Lg~~~~V~as~GHi~dl~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~v~~lk~~ak--~ad~v~lAtD~DR 88 (570)
T COG0550 13 KTIAKYLGKGYVVTASVGHLRDLPFPEEYKGWVDVDLPIFEPKYIIKPGKKKKVVKKLKKLAK--KADEVYLATDPDR 88 (570)
T ss_pred HHHHHhcCCCcEEEEcccccccCCChhhccCCcCCcccccccceeccchhhHHHHHHHHHHhc--cCCEEEECCCCCc
Confidence 45889999988744 99985442 11111111 1 0111 2333344444433 5999999999954
No 28
>PF01248 Ribosomal_L7Ae: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; InterPro: IPR004038 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, ribosomal protein L30 from eukaryotes and archaebacteria, Gadd45 and MyD118 [].; PDB: 2CZW_A 3V7E_B 2QEX_F 1YJ9_F 1VQ8_F 1YJN_F 3I56_F 1VQ6_F 2OTJ_F 1YIJ_F ....
Probab=29.89 E-value=1.1e+02 Score=25.94 Aligned_cols=44 Identities=23% Similarity=0.320 Sum_probs=31.9
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhhHHH-HHHHHhhcCceeEEEeCC
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESETSL-LQSLVVLNGKTIALVKRP 483 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E~~e-Lk~lL~~~g~~v~vv~r~ 483 (563)
+++.+.+++-+++-|++|.|.++..... |..+=. ...+|+++-+
T Consensus 21 ~~v~k~l~~~~~~lvilA~d~~~~~~~~~l~~~c~--~~~Ip~~~~~ 65 (95)
T PF01248_consen 21 KEVLKALKKGKAKLVILAEDCSPDSIKKHLPALCE--EKNIPYVFVP 65 (95)
T ss_dssp HHHHHHHHTTCESEEEEETTSSSGHHHHHHHHHHH--HTTEEEEEES
T ss_pred HHHHHHHHcCCCcEEEEcCCCChhhhcccchhhee--ccceeEEEEC
Confidence 4556666666899999999998877777 555544 2457777665
No 29
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=28.90 E-value=30 Score=33.12 Aligned_cols=21 Identities=24% Similarity=0.567 Sum_probs=14.3
Q ss_pred ccccc-CCCCeEEEEEcCCCCc
Q 008526 206 TVEWK-PKSDKFLFAICLSGQM 226 (563)
Q Consensus 206 ~~~w~-p~~gy~l~cpCmgGnq 226 (563)
+..|+ ..+....+|||+|++.
T Consensus 114 ~~~~~~~~~~~~~~CPCHGS~y 135 (177)
T COG0723 114 TVPWNNAGAEGGFFCPCHGSRY 135 (177)
T ss_pred ccCcccCCCCCeEEccCCCCeE
Confidence 34564 2246779999999663
No 30
>cd08193 HVD 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. 5-hydroxyvalerate dehydrogenase (HVD) is an iron-containing (type III) NAD-dependent alcohol dehydrogenase. It plays a role in the cyclopentanol metabolism biochemical pathway. It catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. This cyclopentanol (cpn) degradation pathway is present in some bacteria which can use cyclopentanol as sole carbon source. In Comamonas sp. strain NCIMB 9872, this enzyme is encoded by the CpnD gene.
Probab=28.57 E-value=2.4e+02 Score=30.08 Aligned_cols=40 Identities=15% Similarity=0.110 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCC--h-hhHHHHHHHHhhcC
Q 008526 435 QAADCITRLAERAKAPVIYLSTDAA--E-SETSLLQSLVVLNG 474 (563)
Q Consensus 435 ~aa~qI~~~vk~~~lk~VFIATDA~--~-~E~~eLk~lL~~~g 474 (563)
++.++|...+++.+.++++|-||.. + ...+.++..|..++
T Consensus 12 g~l~~l~~~l~~~~~~~~livt~~~~~~~~~~~~v~~~L~~~~ 54 (376)
T cd08193 12 GSLARLGELLAALGAKRVLVVTDPGILKAGLIDPLLASLEAAG 54 (376)
T ss_pred CHHHHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcC
Confidence 4667888888888989999999985 2 24677888886433
No 31
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....
Probab=27.92 E-value=96 Score=26.67 Aligned_cols=23 Identities=30% Similarity=0.328 Sum_probs=14.7
Q ss_pred HHHHHHHHH-cCCCEEEEecCCCh
Q 008526 438 DCITRLAER-AKAPVIYLSTDAAE 460 (563)
Q Consensus 438 ~qI~~~vk~-~~lk~VFIATDA~~ 460 (563)
++|+.+.+. .+.+.|+||||++.
T Consensus 48 ~~i~~l~~~~~~~~~iiiatD~D~ 71 (100)
T PF01751_consen 48 KQIKNLKKLLKKADEIIIATDPDR 71 (100)
T ss_dssp HHHHHHHHHHHSCSEEEEEC-SSH
T ss_pred ccchhhHHHhhhccEeeecCCCCh
Confidence 334444444 46999999999955
No 32
>PRK09190 hypothetical protein; Provisional
Probab=27.72 E-value=1.7e+02 Score=29.84 Aligned_cols=46 Identities=13% Similarity=0.169 Sum_probs=33.9
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhh----cCceeEEEeCC
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESETSLLQSLVVL----NGKTIALVKRP 483 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~----~g~~v~vv~r~ 483 (563)
.++...+++-++.-|++|+|+.+...+.|.++-.. .+..||++..+
T Consensus 117 ~~V~~alk~gk~~Lvi~A~DaS~~t~kKl~~~~~~~~~~~~~~Vp~v~~~ 166 (220)
T PRK09190 117 EKVDAALRSGEAAALIHASDGAADGKRKLDQARRALVHETGREIPVIGLF 166 (220)
T ss_pred HHHHHHHHcCCceEEEEeccCChhHHHHHHHHHHhhcccccCCccEEEec
Confidence 45666677778999999999999999999887741 01446666555
No 33
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=27.29 E-value=42 Score=36.14 Aligned_cols=65 Identities=18% Similarity=0.242 Sum_probs=34.2
Q ss_pred CeEEEE-EcCCCCcccchhhhhhhhHHHHHhcCEEecCCCcccc---ccceeeec--hhhhhhhCCcceeeHHH
Q 008526 214 DKFLFA-ICLSGQMSNHLICLEKHMFLAALLNRVLVIPSSKFDY---QYSRVLDI--EHINDCLGRKVVVSFEN 281 (563)
Q Consensus 214 gy~l~c-pCmgGnqanHflcleg~l~FAk~LNRTLVLPPw~i~Y---~f~~fFDV--esL~~y~~~~~VIemEe 281 (563)
+.+|.| ||.| +.|-|.+|-..-.+|+-.+||||+-=-.--| ||.+-|.+ |+++.- ++++||-=++
T Consensus 2 ~r~~~~r~r~g--~gd~l~~la~aw~~a~~~~r~l~idw~~s~~~~~~f~n~f~~ffepv~~i-~~~~~~~~d~ 72 (321)
T PF05830_consen 2 QRFVVSRRRTG--LGDCLWSLAAAWRYAKRTGRTLVIDWRGSCYLDQPFTNAFPVFFEPVEDI-AGVRVICDDR 72 (321)
T ss_dssp --EEEEE--S---HHHHHHHHHHHHHHHHHHT-EEEEE-BT-TT-SSTTSBSHHHHB---SEE-TTEEEE-SGG
T ss_pred CceEEEeccCC--chhHHHHHHHHHHHHHHhCCeEEEEcCCceecCCcccccCCcccchhhhh-cCceeEecch
Confidence 556666 6766 2457888889999999999999985211123 44433332 445443 5667774333
No 34
>TIGR02195 heptsyl_trn_II lipopolysaccharide heptosyltransferase II. This family consists of examples of ADP-heptose:LPS heptosyltransferase II, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria.
Probab=26.96 E-value=3.1e+02 Score=28.10 Aligned_cols=57 Identities=18% Similarity=0.253 Sum_probs=31.8
Q ss_pred CCCcEEeeeechhhhhhccCCCCCCCCChHHHHHHHHHHHHHcCCCEEEEecCCChhhHHHHHHHH
Q 008526 405 GSNFIALHFRRHGFLKFCNAKKPSCFYPIPQAADCITRLAERAKAPVIYLSTDAAESETSLLQSLV 470 (563)
Q Consensus 405 ggpYIgVHLRR~DF~~ac~~~vPsC~psi~~aa~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL 470 (563)
++|||++|.=-. |- |.-..|.+.-++-++.+.+ .+.+.|.+.+.++....+++.+.+
T Consensus 173 ~~~~i~i~pga~-~~-------~~K~Wp~e~~~~li~~l~~-~~~~ivl~G~~~e~~~~~~i~~~~ 229 (334)
T TIGR02195 173 ERPIIAFCPGAE-FG-------PAKRWPHEHYAELAKRLID-QGYQVVLFGSAKDHPAGNEIEALL 229 (334)
T ss_pred CCCEEEEcCCCC-CC-------ccCCCCHHHHHHHHHHHHH-CCCEEEEEEChhhHHHHHHHHHhC
Confidence 469999996211 11 1112235555555555444 478889888877444455565554
No 35
>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region). Portion of beta integrins that lies N-terminal to their EGF-like repeats. Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Beta integrins are proposed to have a von Willebrand factor type-A "insert" or "I" -like domain (although this remains to be confirmed).
Probab=26.18 E-value=1.4e+02 Score=33.54 Aligned_cols=53 Identities=17% Similarity=0.177 Sum_probs=39.1
Q ss_pred eeeech-hhhhhccCCCCCCCCChHHHHHHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHh
Q 008526 411 LHFRRH-GFLKFCNAKKPSCFYPIPQAADCITRLAERAKAPVIYLSTDAAESETSLLQSLVV 471 (563)
Q Consensus 411 VHLRR~-DF~~ac~~~vPsC~psi~~aa~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~ 471 (563)
.||... -+-..-..|=|| + .||.+++.+.++..||.-|....+-.++|.++++
T Consensus 260 CHL~~~g~Yt~s~~~DYPS----i----~ql~~kL~e~nI~~IFAVT~~~~~~Y~~Ls~lip 313 (423)
T smart00187 260 CHLDNNGEYTMSTTQDYPS----I----GQLNQKLAENNINPIFAVTKKQVSLYKELSALIP 313 (423)
T ss_pred ceeCCCCCcCccCcCCCCC----H----HHHHHHHHhcCceEEEEEcccchhHHHHHHHhcC
Confidence 466552 333333335476 3 6677888999999999999997788999999996
No 36
>cd08192 Fe-ADH7 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. NAD-dependent iron-containing alcohol dehydrogenase-like. Proteins in this family are NAD-dependent alcohol dehydrogenases which are involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. They catalyze the oxidation of beta-hydroxy CoA ester to beta-oxo CoA ester, which then be subject to CoA-dependent thiolysis to yield acetyl-CoA and 6-C8-SPC-CoA. The major laundry surfactant in worldwide use is commercial linear alkylbenzenesulfonate (LAS) which contains 20 congeners of linear alkanes (C10 to C13). LAS is fully biodegradable in oxic environments. Degradation involves microbial communities. Parvibaculum lavamentivorans DS-1T is a representative member of many heterotrophic, LAS-degrading communities, in which it catalyzes the first steps of LAS degradation. Strain DS-1T is a small heterotrophic bacterium able to omega-oxygenate the comm
Probab=25.29 E-value=3.2e+02 Score=29.04 Aligned_cols=40 Identities=13% Similarity=0.018 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCChh---hHHHHHHHHhhcC
Q 008526 435 QAADCITRLAERAKAPVIYLSTDAAES---ETSLLQSLVVLNG 474 (563)
Q Consensus 435 ~aa~qI~~~vk~~~lk~VFIATDA~~~---E~~eLk~lL~~~g 474 (563)
++.++|-..+++.+.++++|-||..-. ..+++++.|..+|
T Consensus 10 g~~~~l~~~l~~~g~~~~liv~~~~~~~~~~~~~v~~~L~~~g 52 (370)
T cd08192 10 GAIKELPAECAELGIKRPLIVTDPGLAALGLVARVLALLEDAG 52 (370)
T ss_pred CHHHHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcC
Confidence 467788888888898999999997432 4677888886434
No 37
>PF04123 DUF373: Domain of unknown function (DUF373); InterPro: IPR007254 This archaeal family of unknown function is predicted to be an integral membrane protein with six transmembrane regions.
Probab=25.27 E-value=1.3e+02 Score=32.78 Aligned_cols=61 Identities=20% Similarity=0.247 Sum_probs=41.6
Q ss_pred hHHHHHHHHHHHHHcCCCEEEEecCCChhh--HHHHHHHHhhcCceeEEEeCCCCCCchhhhhH
Q 008526 433 IPQAADCITRLAERAKAPVIYLSTDAAESE--TSLLQSLVVLNGKTIALVKRPPRNSAEKWDSL 494 (563)
Q Consensus 433 i~~aa~qI~~~vk~~~lk~VFIATDA~~~E--~~eLk~lL~~~g~~v~vv~r~~~~~~e~~~~l 494 (563)
-..+++|+..++++++.+.+++=||.++.| ++-+|+-++..+-.-+||++ .+.-++++--+
T Consensus 83 d~~I~~qld~vl~~~~~~~~i~VsDGaeDE~vlPiIqSr~~V~sV~RVVVkQ-s~~iEsTYyll 145 (344)
T PF04123_consen 83 DRKIAEQLDEVLSKFDPDSAIVVSDGAEDERVLPIIQSRVPVDSVKRVVVKQ-SRGIESTYYLL 145 (344)
T ss_pred HHHHHHHHHHHHHhCCCCEEEEEecChhhhhhhHhhhccCceEEEEEEEEEc-CCCcHHHHHHH
Confidence 456889999999999999999999998876 66777777532212223443 33434444443
No 38
>cd06382 PBP1_iGluR_Kainate N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Kainate receptors have five subunits, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeri
Probab=24.68 E-value=7e+02 Score=25.05 Aligned_cols=95 Identities=14% Similarity=0.134 Sum_probs=55.3
Q ss_pred CCChHHHHHHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhhcCc---eeEEEeCCCCCCchhhhhHhhhccCCCchhH
Q 008526 430 FYPIPQAADCITRLAERAKAPVIYLSTDAAESETSLLQSLVVLNGK---TIALVKRPPRNSAEKWDSLLYRHHLEDDSQV 506 (563)
Q Consensus 430 ~psi~~aa~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~~g~---~v~vv~r~~~~~~e~~~~ll~kdg~~~Dg~v 506 (563)
.|+-...++.+..+++..+.++|.|-.|.++ ....|+++++..+. .+.+ ...++ ++ .+
T Consensus 110 ~p~~~~~~~a~~~~~~~~~w~~vavl~~~~~-~~~~l~~~~~~~~~~g~~v~~-~~~~~----------------~~-d~ 170 (327)
T cd06382 110 YPSNADLSRAYADIVKSFNWKSFTIIYESAE-GLLRLQELLQAFGISGITITV-RQLDD----------------DL-DY 170 (327)
T ss_pred CCCHHHHHHHHHHHHHhcCCcEEEEEecChH-HHHHHHHHHHhhccCCCeEEE-EEccC----------------Cc-cH
Confidence 3456666777888888889888888888744 56678888864332 2322 22221 11 23
Q ss_pred HHHHhHHHHhcCCccccccccccchHHHHHHHhcCCC
Q 008526 507 EAMLDKTICAMSNVFIGASGSTFTEDIMRLRKDWGST 543 (563)
Q Consensus 507 vAiIDq~Ica~A~~FIGtc~STFS~~IkrERdl~G~p 543 (563)
.++|.++--+.++.+|-.|...=+..+.++=...|..
T Consensus 171 ~~~l~~i~~~~~d~vv~~~~~~~~~~~~~qa~~~g~~ 207 (327)
T cd06382 171 RPLLKEIKNSGDNRIIIDCSADILIELLKQAQQVGMM 207 (327)
T ss_pred HHHHHHHHhcCceEEEEECCHHHHHHHHHHHHHhCcc
Confidence 5777777767777666555433334444333334443
No 39
>COG0803 LraI ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]
Probab=23.73 E-value=3.6e+02 Score=28.11 Aligned_cols=62 Identities=10% Similarity=0.155 Sum_probs=44.8
Q ss_pred CCCcEEeeeechhhhhhccC-CC---------CCCCCChHHHHHHHHHHHHHcCCCEEEEecCCChhhHHHHHHHH
Q 008526 405 GSNFIALHFRRHGFLKFCNA-KK---------PSCFYPIPQAADCITRLAERAKAPVIYLSTDAAESETSLLQSLV 470 (563)
Q Consensus 405 ggpYIgVHLRR~DF~~ac~~-~v---------PsC~psi~~aa~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL 470 (563)
++-+|..| ..|-|.|+. .. |.=.|+..++ ..|.+.+++.+++.||+.+..+....+.|.+-.
T Consensus 192 ~r~~vt~h---~af~Y~~~~~g~~~~~i~~~~~~~e~s~~~l-~~l~~~ik~~~i~~If~e~~~~~~~~~~la~e~ 263 (303)
T COG0803 192 QRDVVTSH---GAFGYLARDYGLKQVAIAGISPEAEPSPKDL-AKLVDLIKKKNIKAIFVESNVSSKSAETLAKET 263 (303)
T ss_pred CcEEEeec---chHHHHHhccCCccccccCcCcccCCCHHHH-HHHHHHHHHcCCCEEEEeCCCChHHHHHHHHHh
Confidence 45677777 467777764 21 1134557777 778888999999999999999877777777765
No 40
>cd08182 HEPD Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP). Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP) with either NADH or NADPH as a cofactor. NADH is the preferred cofactor. PnAA is a biosynthetic intermediate for several phosphonates such as the antibiotic fosfomycin, phosphinothricin tripeptide (PTT), and 2-aminoethylphosphonate (AEP). This enzyme is named PhpC in PTT biosynthesis pathway in Streptomyces hygroscopicus and S. viridochromogenes. Members of this family are only found in bacteria.
Probab=23.40 E-value=3.4e+02 Score=28.75 Aligned_cols=38 Identities=16% Similarity=0.084 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCChhhHHHHHHHHhh
Q 008526 435 QAADCITRLAERAKAPVIYLSTDAAESETSLLQSLVVL 472 (563)
Q Consensus 435 ~aa~qI~~~vk~~~lk~VFIATDA~~~E~~eLk~lL~~ 472 (563)
.+.++|...+++.+.++++|-||..-...+.+++.|+.
T Consensus 9 g~l~~l~~~~~~~g~~~~livtd~~~~~~~~~~~~l~~ 46 (367)
T cd08182 9 GAIAKLPSLLKGLGGKRVLLVTGPRSAIASGLTDILKP 46 (367)
T ss_pred CHHHHHHHHHHhcCCCeEEEEeCchHHHHHHHHHHHHH
Confidence 35677888888888899999999855556778888864
No 41
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=23.35 E-value=1.1e+02 Score=35.64 Aligned_cols=28 Identities=18% Similarity=0.310 Sum_probs=23.6
Q ss_pred hHHHHHHHHHHHHHcCCCEEEEecCCCh
Q 008526 433 IPQAADCITRLAERAKAPVIYLSTDAAE 460 (563)
Q Consensus 433 i~~aa~qI~~~vk~~~lk~VFIATDA~~ 460 (563)
.+.+++.|++++++.+++.||+|||++.
T Consensus 80 ~~~~~~~ik~l~k~~~ad~Ii~AtDpDR 107 (660)
T TIGR01056 80 TKKQFNVIKRILKENKVDEVVIATDPDR 107 (660)
T ss_pred hHHHHHHHHHHhhhcCCCEEEECCCCCc
Confidence 5667788899988778999999999954
No 42
>PRK10017 colanic acid biosynthesis protein; Provisional
Probab=22.87 E-value=2.6e+02 Score=30.94 Aligned_cols=63 Identities=21% Similarity=0.193 Sum_probs=34.3
Q ss_pred CCCcEEeeeechhhhhhccCCC-CCCCCChHHHHHHHHHHHHHcCCCEEEEecC-------CChhh-HHHHHHHHh
Q 008526 405 GSNFIALHFRRHGFLKFCNAKK-PSCFYPIPQAADCITRLAERAKAPVIYLSTD-------AAESE-TSLLQSLVV 471 (563)
Q Consensus 405 ggpYIgVHLRR~DF~~ac~~~v-PsC~psi~~aa~qI~~~vk~~~lk~VFIATD-------A~~~E-~~eLk~lL~ 471 (563)
.+++|||=+|. |...-+... ..+-+ .+.+++.+..++++ |.++|||++= .++.+ ..+|.+.++
T Consensus 233 ~~~~Vgisvr~--~~~~~~~~~~~~~~Y-~~~la~~i~~Li~~-g~~Vv~lp~~~~~~~~~~dD~~~~~~l~~~~~ 304 (426)
T PRK10017 233 QQKTVAITLRE--LAPFDKRLGTTQQAY-EKAFAGVVNRIIDE-GYQVIALSTCTGIDSYNKDDRMVALNLRQHVS 304 (426)
T ss_pred cCCEEEEEecc--cccccccccccHHHH-HHHHHHHHHHHHHC-CCeEEEEecccCccCCCCchHHHHHHHHHhcc
Confidence 45899999994 332211100 00000 34566666666655 9999999972 32333 355666664
No 43
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=22.72 E-value=1.7e+02 Score=27.05 Aligned_cols=44 Identities=27% Similarity=0.329 Sum_probs=30.7
Q ss_pred HHHHHHHHHcCCCEEEEecCCChhh-HHHHHHHHhhcCceeEEEeCC
Q 008526 438 DCITRLAERAKAPVIYLSTDAAESE-TSLLQSLVVLNGKTIALVKRP 483 (563)
Q Consensus 438 ~qI~~~vk~~~lk~VFIATDA~~~E-~~eLk~lL~~~g~~v~vv~r~ 483 (563)
+++.+.+++-+++-|+||.|+++.+ ...+..+=. ...||++...
T Consensus 36 ~~v~kaikkgkakLVilA~D~s~~~i~~~~~~lc~--~~~Vp~~~~~ 80 (122)
T PRK04175 36 NETTKAVERGIAKLVVIAEDVDPEEIVAHLPLLCE--EKKIPYVYVP 80 (122)
T ss_pred HHHHHHHHcCCccEEEEeCCCChHHHHHHHHHHHH--HcCCCEEEEC
Confidence 5566666777899999999996655 466666654 2456666655
No 44
>cd08551 Fe-ADH iron-containing alcohol dehydrogenases (Fe-ADH)-like. Large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. They contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases: Zinc-containing long-chain alcohol dehydrogenases; insect-type, or short-chain alcohol dehydrogenases; iron-containing alcohol dehydrogenases, and others. The iron-containing family has a Rossmann fold-like topology that resembles the fold of the zinc-dependent alcohol dehydrogenases, but lacks sequence homology, and differs in strand arrangement. ADH catalyzes the reversible oxidation of alcohol to acetaldehyde with the simultaneous reduction of NAD(P)+ to NAD(P)H.
Probab=22.18 E-value=3.8e+02 Score=28.35 Aligned_cols=40 Identities=10% Similarity=0.001 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCCh---hhHHHHHHHHhhcC
Q 008526 435 QAADCITRLAERAKAPVIYLSTDAAE---SETSLLQSLVVLNG 474 (563)
Q Consensus 435 ~aa~qI~~~vk~~~lk~VFIATDA~~---~E~~eLk~lL~~~g 474 (563)
.+.++|...+++++.++++|-||..- ...+.+.+.|+.++
T Consensus 9 g~l~~l~~~l~~~~~~~~lvv~~~~~~~~~~~~~v~~~L~~~~ 51 (370)
T cd08551 9 GAIEKLGEEIKNLGGRKALIVTDPGLVKTGVLDKVIDSLKEAG 51 (370)
T ss_pred CHHHHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcC
Confidence 46678888888889999999999743 23457888886433
No 45
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=21.63 E-value=8.1e+02 Score=25.16 Aligned_cols=89 Identities=13% Similarity=0.194 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCCh---hhHHHHHHHHhhcCceeEEEeCCCCCCchhhhhHhhhccCCCchhHHHHHh
Q 008526 435 QAADCITRLAERAKAPVIYLSTDAAE---SETSLLQSLVVLNGKTIALVKRPPRNSAEKWDSLLYRHHLEDDSQVEAMLD 511 (563)
Q Consensus 435 ~aa~qI~~~vk~~~lk~VFIATDA~~---~E~~eLk~lL~~~g~~v~vv~r~~~~~~e~~~~ll~kdg~~~Dg~vvAiID 511 (563)
++...+..++++.+.++|+|-++.+. ...+.+++.++..|-.+.....++. +..++.++|.
T Consensus 119 ~~~~~~~~~~~~~g~k~vaii~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~----------------~~~D~~~~v~ 182 (348)
T cd06355 119 QIIPAVDWLMSNKGGKRFYLVGSDYVYPRTANKILKAQLESLGGEVVGEEYLPL----------------GHTDFQSIIN 182 (348)
T ss_pred hHHHHHHHHHhccCCCeEEEECCcchHHHHHHHHHHHHHHHcCCeEEeeEEecC----------------ChhhHHHHHH
Confidence 34444444455557888887765532 4456677777654533323233321 1223457777
Q ss_pred HHHHhcCCccc-cccccccchHHHHHHHh
Q 008526 512 KTICAMSNVFI-GASGSTFTEDIMRLRKD 539 (563)
Q Consensus 512 q~Ica~A~~FI-Gtc~STFS~~IkrERdl 539 (563)
++.-+.++..| +........+++..|+.
T Consensus 183 ~l~~~~pd~v~~~~~~~~~~~~~~~~~~~ 211 (348)
T cd06355 183 KIKAAKPDVVVSTVNGDSNVAFFKQLKAA 211 (348)
T ss_pred HHHHhCCCEEEEeccCCchHHHHHHHHHc
Confidence 77777777643 33444445566666654
No 46
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=20.78 E-value=2e+02 Score=24.12 Aligned_cols=44 Identities=20% Similarity=0.409 Sum_probs=27.1
Q ss_pred CCCcchHHHHHHHhhhhhhHHHHHHHHhCCCccCCCCCCCCcccCccccccccCCCCCccccccCCCCeEEEEE
Q 008526 147 TNNPFFQEAKSVLLNQISLNRQIEQILLSPHKVSNFTPNDAVWGLESCRKIDSIIPNKRTVEWKPKSDKFLFAI 220 (563)
Q Consensus 147 ~~~~~~~~~~sal~~qi~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~w~p~~gy~l~cp 220 (563)
+-+++++|+-+.+. +.++..+.+.|- +-..|+|||.+|.|.|=|
T Consensus 18 ~~Plt~~eI~d~l~--~d~~~~~~~~Lk----------------------------~npKI~~d~~~~~f~fkp 61 (65)
T PF02186_consen 18 DHPLTLEEILDYLS--LDIGKKLKQWLK----------------------------NNPKIEYDPDGNTFSFKP 61 (65)
T ss_dssp -S-B-HHHHHHHHT--SSS-HHHHHHHH----------------------------H-TTEEEE-TT-CEEE--
T ss_pred CCCcCHHHHHHHHc--CCCCHHHHHHHH----------------------------cCCCEEEecCCCEEEecc
Confidence 34679999999998 777888888883 223577888655888754
No 47
>PF13728 TraF: F plasmid transfer operon protein
Probab=20.03 E-value=1.4e+02 Score=29.91 Aligned_cols=82 Identities=26% Similarity=0.405 Sum_probs=59.0
Q ss_pred CcccccccccccccHHHHHHHHHHHH----HhhCCCcEEeeeech--hh-----hhhccCC------------------C
Q 008526 376 GPINHRCKTLIEPSRLIMVTAQRFVQ----TFLGSNFIALHFRRH--GF-----LKFCNAK------------------K 426 (563)
Q Consensus 376 ~Pv~~k~rkyL~wS~~I~~~A~~fI~----~aLggpYIgVHLRR~--DF-----~~ac~~~------------------v 426 (563)
.|-.+..++|+.+.+-++..|.+|=. ..+..|.+.-=+|+- -+ ......+ .
T Consensus 50 ~PT~eNv~~y~~lq~~~~dka~~Fa~~~~~v~l~~P~Ld~~~~~P~~~~a~~~~~~~~~~~~~~~l~~la~~~gL~~F~~ 129 (215)
T PF13728_consen 50 NPTPENVRAYLRLQRFAMDKASRFADTWQRVLLQNPELDYTLRRPVSNFARQAYLRQREQKRDKALKQLAQKYGLFFFYR 129 (215)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHhhCeEEEEEEc
Confidence 35555556999999999999999875 456778877777772 22 1111110 1
Q ss_pred CCCCCChHHHHHHHHHHHHHcCCCEEEEecCC
Q 008526 427 PSCFYPIPQAADCITRLAERAKAPVIYLSTDA 458 (563)
Q Consensus 427 PsC~psi~~aa~qI~~~vk~~~lk~VFIATDA 458 (563)
++|-+.-.++ .-|+.+.+++|+++++|+.|.
T Consensus 130 ~~C~~C~~~~-pil~~~~~~yg~~v~~vs~DG 160 (215)
T PF13728_consen 130 SDCPYCQQQA-PILQQFADKYGFSVIPVSLDG 160 (215)
T ss_pred CCCchhHHHH-HHHHHHHHHhCCEEEEEecCC
Confidence 5588776665 888899999999999999996
Done!