Query 020973
Match_columns 319
No_of_seqs 134 out of 218
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 06:36:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020973.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020973hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14144 DOG1: Seed dormancy c 100.0 3E-31 6.6E-36 209.8 5.0 75 100-176 1-79 (80)
2 PF13801 Metal_resist: Heavy-m 96.4 0.045 9.8E-07 43.5 10.3 86 188-282 39-124 (125)
3 PRK12750 cpxP periplasmic repr 95.9 0.51 1.1E-05 42.5 15.3 99 188-296 50-157 (170)
4 COG3678 CpxP P pilus assembly/ 95.9 0.12 2.5E-06 46.3 11.0 88 188-287 55-142 (160)
5 PRK10455 periplasmic protein; 95.1 0.43 9.2E-06 42.6 11.9 94 188-297 54-148 (161)
6 PRK10363 cpxP periplasmic repr 94.7 0.98 2.1E-05 40.9 13.0 101 188-301 48-149 (166)
7 PRK12751 cpxP periplasmic stre 93.9 1.5 3.2E-05 39.5 12.4 99 188-299 54-153 (162)
8 PF07813 LTXXQ: LTXXQ motif fa 91.4 1.5 3.2E-05 34.2 8.1 80 188-284 12-96 (100)
9 PF05227 CHASE3: CHASE3 domain 52.2 57 0.0012 26.4 6.5 77 52-128 5-81 (138)
10 PRK01026 tetrahydromethanopter 42.6 19 0.00041 29.0 2.0 25 50-74 12-36 (77)
11 PF12004 DUF3498: Domain of un 39.1 10 0.00022 39.8 0.0 61 39-108 420-480 (495)
12 PF03371 PRP38: PRP38 family; 37.2 29 0.00064 31.3 2.7 25 166-199 62-86 (172)
13 TIGR01149 mtrG N5-methyltetrah 35.4 29 0.00064 27.4 2.0 25 50-74 9-33 (70)
14 PF04362 Iron_traffic: Bacteri 34.8 93 0.002 25.6 4.9 43 84-127 32-74 (88)
15 PF06013 WXG100: Proteins of 1 34.5 1.8E+02 0.0038 21.1 6.2 49 52-106 20-68 (86)
16 COG3130 Rmf Ribosome modulatio 33.1 16 0.00035 27.3 0.3 12 158-169 37-48 (55)
17 PHA02414 hypothetical protein 33.0 1.3E+02 0.0029 25.4 5.6 44 53-111 4-47 (111)
18 PF11459 DUF2893: Protein of u 32.4 1.1E+02 0.0024 24.0 4.8 41 251-292 21-61 (69)
19 PF04210 MtrG: Tetrahydrometha 31.0 37 0.00081 26.8 2.0 24 51-74 10-33 (70)
20 PRK14563 ribosome modulation f 30.7 13 0.00028 28.1 -0.6 15 152-168 33-47 (55)
21 PF00589 Phage_integrase: Phag 26.8 26 0.00057 28.7 0.5 21 158-178 28-48 (173)
22 PF13586 DDE_Tnp_1_2: Transpos 25.3 30 0.00064 27.0 0.6 19 148-167 44-62 (88)
No 1
>PF14144 DOG1: Seed dormancy control
Probab=99.97 E-value=3e-31 Score=209.77 Aligned_cols=75 Identities=29% Similarity=0.594 Sum_probs=70.0
Q ss_pred hhHHHHHHhccc----chHHHHHHHHHHHHHHHHHhccCccccccccccccCCCCCChhhhhhhhhhcCCchhHHHHHHh
Q 020973 100 TRAVSLEKQLNS----RWELEELIKEQLNRFNTHYNHSSIPTYLKDVASFLMPRWTPPHELAALYWIGDWRPSAILDLAR 175 (319)
Q Consensus 100 r~l~eLr~Al~s----d~eL~~LV~~~l~Hy~e~y~~~Ks~aA~~DVf~llsp~W~tplEra~FLWiGGfRPS~llkLL~ 175 (319)
|++.|||+|+++ |.+|+.||+++|+||.+|| ++|+.+|++|||++|+|+|+||+|| ||+||||||||++|+|||
T Consensus 1 ~~l~eLr~al~~~~~~~~~L~~lV~~~~~Hy~~y~-~~K~~aa~~DV~~~~s~~W~sp~Er-~flWiGG~RPS~~~~ll~ 78 (80)
T PF14144_consen 1 RQLNELRAALQSHADSDDELRSLVDKVMSHYDEYY-RAKSAAAKADVFHLLSPPWKSPLER-CFLWIGGWRPSELFKLLY 78 (80)
T ss_pred CcHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHhcchHHHhCCCCCCHHHH-HHHHHhcCCHHHHHHHHh
Confidence 578999999943 7899999999999999755 5799999999999999999999999 999999999999999999
Q ss_pred h
Q 020973 176 G 176 (319)
Q Consensus 176 s 176 (319)
+
T Consensus 79 s 79 (80)
T PF14144_consen 79 S 79 (80)
T ss_pred c
Confidence 7
No 2
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=96.43 E-value=0.045 Score=43.50 Aligned_cols=86 Identities=21% Similarity=0.200 Sum_probs=68.0
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhhhhhHHHHHHHHHHHHHHHHHHhHHHHHH
Q 020973 188 SKSESSDAERLLSQVMHEIRIEEAIIDEEMAEIQATCVLHLPFASLNKKRLYGSALGFIQKEFKKIERVIIKAQQLRLKA 267 (319)
Q Consensus 188 ~L~LTeqQl~~I~~Lq~st~qaEdaLsq~ma~lQqslA~d~~~~~~~~~~~g~~A~~~a~~kl~~Le~~l~qAD~LR~~T 267 (319)
.++||++|...|..+.......-..+-+.+......+. ....++.. - ...+...++.+...-.+.+..|.++
T Consensus 39 ~l~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l~-~ll~~~~~----D---~~~i~a~~~~~~~~~~~l~~~~~~~ 110 (125)
T PF13801_consen 39 MLNLTPEQQAKLRALMDEFRQEMRALRQELRAARQELR-ALLAAPPP----D---EAAIEALLEEIREAQAELRQERLEH 110 (125)
T ss_dssp HS-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCSSS--------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHcCCCC----C---HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35699999999999999999999999999998888887 44322211 1 2247777788888888899999999
Q ss_pred HHHHHHhhCCHHHHH
Q 020973 268 LELVVKKVLSPTDAA 282 (319)
Q Consensus 268 L~~lv~~ILTp~QAA 282 (319)
+.++. .+|||.|=+
T Consensus 111 ~~~~~-~~LtpeQR~ 124 (125)
T PF13801_consen 111 LLEIR-AVLTPEQRA 124 (125)
T ss_dssp HHHHH-HTT-GGGHH
T ss_pred HHHHH-HcCCHHHhC
Confidence 99999 999999855
No 3
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=95.91 E-value=0.51 Score=42.46 Aligned_cols=99 Identities=15% Similarity=0.151 Sum_probs=57.2
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHhcccccc-cccccchhhhhhHHHHHHHHHHHHHHHH
Q 020973 188 SKSESSDAERLLSQVMHEIRIEEAI--------IDEEMAEIQATCVLHLPF-ASLNKKRLYGSALGFIQKEFKKIERVII 258 (319)
Q Consensus 188 ~L~LTeqQl~~I~~Lq~st~qaEda--------Lsq~ma~lQqslA~d~~~-~~~~~~~~g~~A~~~a~~kl~~Le~~l~ 258 (319)
.|+||++|...|..++...+.+=.+ ....|....+.+. .+.. .++. ..+ +.+..+.+...-.
T Consensus 50 ~L~LTdeQk~qik~i~~~~r~~~k~~~~~~r~~~~~~m~a~~~~~~-~Ll~a~~FD-----eaa---vral~~~~~~~~~ 120 (170)
T PRK12750 50 QLDLTDAQKEQLKEMREANRAEMKAKYSGNREQSHAEMKAHHAKVQ-ALVLADDFD-----EAA---ANDLAKQMVEKQV 120 (170)
T ss_pred hCCCCHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHH-HHHhcCCCC-----HHH---HHHHHHHHHHHHH
Confidence 6889999999999998777664333 3344444444433 2221 2221 111 2222222222222
Q ss_pred HHhHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH
Q 020973 259 KAQQLRLKALELVVKKVLSPTDAAKFFVAFERIQNAIH 296 (319)
Q Consensus 259 qAD~LR~~TL~~lv~~ILTp~QAA~fLlA~~e~~~rLR 296 (319)
+.---|.++.++++ .||||-|=+.|---..+.....+
T Consensus 121 e~~v~~~~~~~~~~-~vLTpEQRak~~e~~~~r~~~~~ 157 (170)
T PRK12750 121 ERRVKMLEKRHQML-SILTPEQKAKFQELQQERMQECQ 157 (170)
T ss_pred HHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHH
Confidence 22234677999999 99999999999877555544333
No 4
>COG3678 CpxP P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein [Intracellular trafficking and secretion / Cell motility and secretio / Signal transduction mechanisms / Inorganic ion transport and metabolism]
Probab=95.87 E-value=0.12 Score=46.35 Aligned_cols=88 Identities=17% Similarity=0.142 Sum_probs=60.2
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhhhhhHHHHHHHHHHHHHHHHHHhHHHHHH
Q 020973 188 SKSESSDAERLLSQVMHEIRIEEAIIDEEMAEIQATCVLHLPFASLNKKRLYGSALGFIQKEFKKIERVIIKAQQLRLKA 267 (319)
Q Consensus 188 ~L~LTeqQl~~I~~Lq~st~qaEdaLsq~ma~lQqslA~d~~~~~~~~~~~g~~A~~~a~~kl~~Le~~l~qAD~LR~~T 267 (319)
.+.||++|...|..+...-+ .+..+-+..-...+- .++.++.. . ...+....+.++..-.+.+.+|.++
T Consensus 55 ~l~lT~~Qrqqi~~i~~~~~---~a~~~~~~~~r~~l~-~li~a~~~----D---~aka~a~~~~m~~~~~~~~~~r~k~ 123 (160)
T COG3678 55 GLDLTRAQRQQIRDLMQAQR---RAQREQLRSKRRALH-ELIAADQF----D---EAKARAQAEKMENQRQALRELRVKS 123 (160)
T ss_pred cccccHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH-HHHhcCCc----C---HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56799999999999877666 333333333333333 22211111 1 2257777888999999999999999
Q ss_pred HHHHHHhhCCHHHHHHHHHH
Q 020973 268 LELVVKKVLSPTDAAKFFVA 287 (319)
Q Consensus 268 L~~lv~~ILTp~QAA~fLlA 287 (319)
-.++. .||||.|.+.|=--
T Consensus 124 ~~~m~-~vLTPEQr~~l~~~ 142 (160)
T COG3678 124 DNQMY-QVLTPEQRAKLQEL 142 (160)
T ss_pred HHHHH-HhcCHHHHHHHHHH
Confidence 99999 99999999765433
No 5
>PRK10455 periplasmic protein; Reviewed
Probab=95.14 E-value=0.43 Score=42.64 Aligned_cols=94 Identities=11% Similarity=0.150 Sum_probs=59.3
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHhcccccccccccchhhhhhHHHHHHHHHHHHHHHHHHhHHHHH
Q 020973 188 SKSESSDAERLLSQVMHEIRIEEAII-DEEMAEIQATCVLHLPFASLNKKRLYGSALGFIQKEFKKIERVIIKAQQLRLK 266 (319)
Q Consensus 188 ~L~LTeqQl~~I~~Lq~st~qaEdaL-sq~ma~lQqslA~d~~~~~~~~~~~g~~A~~~a~~kl~~Le~~l~qAD~LR~~ 266 (319)
.|.||++|...|..|.+..+..-... -++...++.-++. +++. . +.+...++.+...-.+.-..|.+
T Consensus 54 ~L~LT~~Qrqqir~im~~~r~~~~~~~~~~r~~l~~li~a----d~FD-----e---aavra~~~k~~~~~~~~~~~~~~ 121 (161)
T PRK10455 54 GLNLTDAQKQQIRDIMKAQRDQMKRPPLEERRAMHDIIAS----DTFD-----K---AKAEAQITKMEAQRKARMLAHME 121 (161)
T ss_pred hCCCCHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHcc----CccC-----H---HHHHHHHHHHHHHHHHHHHHHHH
Confidence 68899999999999987766653333 2344444444331 1111 1 12444445555555555557889
Q ss_pred HHHHHHHhhCCHHHHHHHHHHHHHHHHHHHH
Q 020973 267 ALELVVKKVLSPTDAAKFFVAFERIQNAIHQ 297 (319)
Q Consensus 267 TL~~lv~~ILTp~QAA~fLlA~~e~~~rLR~ 297 (319)
+-.+|. .||||-|=+.|=- .+..|+..
T Consensus 122 ~~~qiy-~vLTPEQr~q~~~---~~ekr~~~ 148 (161)
T PRK10455 122 TQNKIY-NVLTPEQKKQFNA---NFEKRLTE 148 (161)
T ss_pred HHHHHH-HhCCHHHHHHHHH---HHHHHHHh
Confidence 999999 9999999998753 34444444
No 6
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=94.69 E-value=0.98 Score=40.89 Aligned_cols=101 Identities=13% Similarity=0.195 Sum_probs=62.6
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhcccccccccccchhhhhhHHHHHHHHHHHHHHHHHHhHHHHH
Q 020973 188 SKSESSDAERLLSQVMHEIRIEEAIID-EEMAEIQATCVLHLPFASLNKKRLYGSALGFIQKEFKKIERVIIKAQQLRLK 266 (319)
Q Consensus 188 ~L~LTeqQl~~I~~Lq~st~qaEdaLs-q~ma~lQqslA~d~~~~~~~~~~~g~~A~~~a~~kl~~Le~~l~qAD~LR~~ 266 (319)
.|.||++|...|-.|.+.-+.+.+.++ .+++.++.-+. .+++ -.. .|.+.++.+...=.+.-=-|.+
T Consensus 48 gLdLTdaQRqQmRdLm~~~r~~~~~~~~~er~amh~LI~----ad~F-----DEa---avra~a~kma~~~~e~~Vem~k 115 (166)
T PRK10363 48 GISLTEHQRQQMRDLMQQARHEQPPVNVSEMETMHRLVT----AENF-----DEN---AVRAQAEKMAQEQVARQVEMAK 115 (166)
T ss_pred CCCCCHHHHHHHHHHHHHHHhcccccCHHHHHHHHHHHh----cCCC-----CHH---HHHHHHHHHHHHHHHHHHHHHH
Confidence 678999999999999988887655543 24445543322 1111 122 2344444443333333335678
Q ss_pred HHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 020973 267 ALELVVKKVLSPTDAAKFFVAFERIQNAIHQVSEQ 301 (319)
Q Consensus 267 TL~~lv~~ILTp~QAA~fLlA~~e~~~rLR~lgs~ 301 (319)
+-++|. .||||-|-+.|=--.-+....+|.++..
T Consensus 116 ~~nqmy-~lLTPEQKaq~~~~~~~rm~~~~~~~~~ 149 (166)
T PRK10363 116 VRNQMY-RLLTPEQQAVLNEKHQQRMEQLRDVTQW 149 (166)
T ss_pred HHHHHH-HhCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 899999 9999999999955444444555555433
No 7
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=93.91 E-value=1.5 Score=39.45 Aligned_cols=99 Identities=8% Similarity=0.107 Sum_probs=64.3
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHhcccccccccccchhhhhhHHHHHHHHHHHHHHHHHHhHHHHH
Q 020973 188 SKSESSDAERLLSQVMHEIRIEEA-IIDEEMAEIQATCVLHLPFASLNKKRLYGSALGFIQKEFKKIERVIIKAQQLRLK 266 (319)
Q Consensus 188 ~L~LTeqQl~~I~~Lq~st~qaEd-aLsq~ma~lQqslA~d~~~~~~~~~~~g~~A~~~a~~kl~~Le~~l~qAD~LR~~ 266 (319)
.+.||++|...|-.+....+.... ..-..++.++.-+. .-+ +. .. .+.+.++.+...-..---.+.+
T Consensus 54 ~l~LTd~QR~qmr~im~~~r~~~~~~~~~~~~~m~~Li~-Ad~---FD-----ea---Avra~~~kma~~~~e~~v~~~~ 121 (162)
T PRK12751 54 GINLTEQQRQQMRDLMRQSHQSQPRLDLEDREAMHKLIT-ADK---FD-----EA---AVRAQAEKMSQNQIERHVEMAK 121 (162)
T ss_pred cCCCCHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHh-cCC---CC-----HH---HHHHHHHHHHHHHHHHHHHHHH
Confidence 678999999999999877776531 12235555555555 222 21 22 2334444444444444446788
Q ss_pred HHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHH
Q 020973 267 ALELVVKKVLSPTDAAKFFVAFERIQNAIHQVS 299 (319)
Q Consensus 267 TL~~lv~~ILTp~QAA~fLlA~~e~~~rLR~lg 299 (319)
+.++++ .+|||-|-+.|=--.-+-...+|...
T Consensus 122 ~~~qmy-~lLTPEQra~l~~~~e~r~~~~~~~~ 153 (162)
T PRK12751 122 VRNQMY-NLLTPEQKEALNKKHQERIEKLQQKP 153 (162)
T ss_pred HHHHHH-HcCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 999999 99999999999777666666666543
No 8
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=91.41 E-value=1.5 Score=34.19 Aligned_cols=80 Identities=11% Similarity=0.182 Sum_probs=46.1
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHhcccccccccccchhhhhhHHHHHH--HHHHHHHHHHHHhH
Q 020973 188 SKSESSDAERLLSQVMHEIRIEEAII---DEEMAEIQATCVLHLPFASLNKKRLYGSALGFIQK--EFKKIERVIIKAQQ 262 (319)
Q Consensus 188 ~L~LTeqQl~~I~~Lq~st~qaEdaL---sq~ma~lQqslA~d~~~~~~~~~~~g~~A~~~a~~--kl~~Le~~l~qAD~ 262 (319)
.|.||++|...+..|....+..-..+ .+.+.++.. . +.. ...+.. .++.+...-.+.-.
T Consensus 12 ~L~LT~eQ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~--~-~~~-------------~~~~~~~~~~~~~~~~~~~~~~ 75 (100)
T PF07813_consen 12 ELNLTDEQKAKWRAIRQAMKAKMKPLKAMREQLRALRD--P-SFD-------------EAAPEALAAMAEMMELRAEMME 75 (100)
T ss_dssp TS--THHHHHHHHHHHHHHCTTS------HHHHHHHHH--S-S---------------HHHHHHHH--HHCHHHHHHHHH
T ss_pred hCCCCHHHHHHHHHHHHHHHHHHHhhcccHHHHHHhcc--c-cCC-------------hhHHHHHHHHHHHHHHHHHHHH
Confidence 67799999999999998887776666 222222222 0 000 001111 11344455555566
Q ss_pred HHHHHHHHHHHhhCCHHHHHHH
Q 020973 263 LRLKALELVVKKVLSPTDAAKF 284 (319)
Q Consensus 263 LR~~TL~~lv~~ILTp~QAA~f 284 (319)
.|..+...+. .||||.|=+.|
T Consensus 76 ~~~~~~~~~~-~vLt~eQk~~~ 96 (100)
T PF07813_consen 76 ERAKAQHALY-AVLTPEQKEKF 96 (100)
T ss_dssp HHHHHHHHHH-TTS-HHHHHHH
T ss_pred HHHHHHHHHH-hcCCHHHHHHH
Confidence 7888999999 99999998765
No 9
>PF05227 CHASE3: CHASE3 domain; InterPro: IPR007891 CHASE3 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are upstream of signal transduction pathways in bacteria. Specifically, CHASE3 domains are found in histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognised by CHASE3 domains are not known at this time [].; PDB: 3VA9_A.
Probab=52.16 E-value=57 Score=26.42 Aligned_cols=77 Identities=10% Similarity=0.069 Sum_probs=53.9
Q ss_pred ccchhHHHHHHHHHHHHHhhhccccCCccccchhhhHHHHHHHHHHHhhhHHHHHHhcccchHHHHHHHHHHHHHHH
Q 020973 52 AGEIDNIVERVENIVERVQCTTIHKSESSKRGEDISREKYSHWRQEQKTRAVSLEKQLNSRWELEELIKEQLNRFNT 128 (319)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~ge~ls~~~Y~~W~eeq~r~l~eLr~Al~sd~eL~~LV~~~l~Hy~e 128 (319)
+..--.|+..+.+++..+-.+-+..-++.=.|+.-+.+-|..+...-...+.+|+..+..+++....++.+-.-+..
T Consensus 5 v~~s~~v~~~~~~l~~~l~~~e~~~RgYlltgd~~~l~~y~~~~~~~~~~l~~L~~l~~~~p~q~~~l~~l~~~~~~ 81 (138)
T PF05227_consen 5 VEHSYEVLRAIEQLESALLDQESALRGYLLTGDPEFLEPYQEARARLEKALAQLRQLVQDNPEQQERLDQLEELIDQ 81 (138)
T ss_dssp ----HHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHcCCHhhhchHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Confidence 33445677777888877777766555566677888899999999999999999999987777666666666655554
No 10
>PRK01026 tetrahydromethanopterin S-methyltransferase subunit G; Provisional
Probab=42.61 E-value=19 Score=28.97 Aligned_cols=25 Identities=28% Similarity=0.478 Sum_probs=22.1
Q ss_pred ccccchhHHHHHHHHHHHHHhhhcc
Q 020973 50 EDAGEIDNIVERVENIVERVQCTTI 74 (319)
Q Consensus 50 ~~~~~~~~~~~~~~~~~~~~q~~~~ 74 (319)
-+..+|..|.+||..|||+|-++.+
T Consensus 12 v~~~d~~~i~~rLD~iEeKVEftn~ 36 (77)
T PRK01026 12 VDPKDFKEIQKRLDEIEEKVEFTNA 36 (77)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999998876
No 11
>PF12004 DUF3498: Domain of unknown function (DUF3498); InterPro: IPR021887 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 433 to 538 amino acids in length. This domain is found associated with PF00616 from PFAM, PF00168 from PFAM. This domain has two conserved sequence motifs: DLQ and PLSFQNP. ; PDB: 3BXJ_B.
Probab=39.06 E-value=10 Score=39.81 Aligned_cols=61 Identities=18% Similarity=0.302 Sum_probs=0.0
Q ss_pred hhhhhccccccccccchhHHHHHHHHHHHHHhhhccccCCccccchhhhHHHHHHHHHHHhhhHHHHHHh
Q 020973 39 DERRVRTGTQREDAGEIDNIVERVENIVERVQCTTIHKSESSKRGEDISREKYSHWRQEQKTRAVSLEKQ 108 (319)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~ge~ls~~~Y~~W~eeq~r~l~eLr~A 108 (319)
-|+|.|- .|-|--+.+..||.||-.+|||+.....+-...+ +-=.+||++|.++|.-|-+|
T Consensus 420 SE~RLr~-QQ~eKd~qmksII~RL~~vEeELrre~~~m~~~~--------~~kqrii~aQ~~~i~~Ldaa 480 (495)
T PF12004_consen 420 SEERLRR-QQEEKDSQMKSIISRLMAVEEELRREHAEMQAVL--------DHKQRIIDAQEKRIAALDAA 480 (495)
T ss_dssp ----------------------------------------------------------------------
T ss_pred hHHHHHH-HhhhhHHHHHHHHhhhhhhhhhhhhhHHHHhccc--------ccchHHHHHhhhhccccccc
Confidence 3444442 4556678899999999999999998887432222 33468999999999998887
No 12
>PF03371 PRP38: PRP38 family; InterPro: IPR005037 Members of this family are related to the pre mRNA splicing factor PRP38 from yeast [], therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation [].
Probab=37.20 E-value=29 Score=31.34 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=21.1
Q ss_pred chhHHHHHHhhhcCCCCCCCCCCCCCcHHHHHHH
Q 020973 166 RPSAILDLARGLVRSPSSISSSSKSESSDAERLL 199 (319)
Q Consensus 166 RPS~llkLL~sl~g~~~~~~~~~L~LTeqQl~~I 199 (319)
|||.+|=|++.++ ++.+|.+|+..+
T Consensus 62 ~Ps~f~CLL~KLl---------~l~pt~~~v~~~ 86 (172)
T PF03371_consen 62 RPSPFFCLLYKLL---------QLRPTKEQVKEL 86 (172)
T ss_pred CCchHHHHHHHHH---------hcccCHHHHHHH
Confidence 6999999999877 677899988764
No 13
>TIGR01149 mtrG N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit G. coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Probab=35.36 E-value=29 Score=27.39 Aligned_cols=25 Identities=20% Similarity=0.449 Sum_probs=21.9
Q ss_pred ccccchhHHHHHHHHHHHHHhhhcc
Q 020973 50 EDAGEIDNIVERVENIVERVQCTTI 74 (319)
Q Consensus 50 ~~~~~~~~~~~~~~~~~~~~q~~~~ 74 (319)
-+..||..+.+||..|||+|-++.+
T Consensus 9 v~~~d~~~i~~rLd~iEeKVEf~~~ 33 (70)
T TIGR01149 9 VEPDEFNEVMKRLDEIEEKVEFVNG 33 (70)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3557899999999999999998876
No 14
>PF04362 Iron_traffic: Bacterial Fe(2+) trafficking; InterPro: IPR007457 The protein represented by this entry, YggX, serves to protect Fe-S clusters from oxidative damage []. The effect is two-fold: proteins that rely on Fe-S clusters do not become inactivated, and the release of free iron and hydrogen peroxide--a DNA damaging agent--is prevented. These observations are consistent with the hypothesis that YggX chelates free iron, and recent experiments show that YggX can indeed bind Fe(II) in vitro and in vivo []. Furthermore, YggX has a positive effect on the action of at least one Fe(II)-responsive protein. The combined actions of YggX is reminiscent of iron trafficking proteins [], and YggX is therefore proposed to play a role in Fe(II) trafficking []. In Escherichia coli, YggX was shown to be under the transcriptional control of the redox-sensing SoxRS system []. ; GO: 0005506 iron ion binding; PDB: 1YHD_A 1T07_A 1XS8_A.
Probab=34.77 E-value=93 Score=25.61 Aligned_cols=43 Identities=21% Similarity=0.426 Sum_probs=34.3
Q ss_pred hhhhHHHHHHHHHHHhhhHHHHHHhcccchHHHHHHHHHHHHHH
Q 020973 84 EDISREKYSHWRQEQKTRAVSLEKQLNSRWELEELIKEQLNRFN 127 (319)
Q Consensus 84 e~ls~~~Y~~W~eeq~r~l~eLr~Al~sd~eL~~LV~~~l~Hy~ 127 (319)
+++|......|+..|...|+|-|=-+ .|.+-|..+..-|..|.
T Consensus 32 ~~iSk~AW~~W~~~QTmLINE~rLn~-~dp~~R~~L~~qM~~Fl 74 (88)
T PF04362_consen 32 DNISKEAWQEWLEHQTMLINEYRLNM-MDPEARKFLEEQMEKFL 74 (88)
T ss_dssp HHSBHHHHHHHHHHHHHHHHHHT--T-TSHHHHHHHHHHHHHHT
T ss_pred HHHhHHHHHHHHHHHHHHHHhccCCC-CCHHHHHHHHHHHHHHh
Confidence 46788999999999999999977544 37788888888888776
No 15
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=34.52 E-value=1.8e+02 Score=21.13 Aligned_cols=49 Identities=20% Similarity=0.447 Sum_probs=26.6
Q ss_pred ccchhHHHHHHHHHHHHHhhhccccCCccccchhhhHHHHHHHHHHHhhhHHHHH
Q 020973 52 AGEIDNIVERVENIVERVQCTTIHKSESSKRGEDISREKYSHWRQEQKTRAVSLE 106 (319)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~ge~ls~~~Y~~W~eeq~r~l~eLr 106 (319)
+.+|++++++|.+..+.+ ...-+|. +-.-+...|..|-....+....|.
T Consensus 20 ~~~l~~~~~~l~~~~~~l--~~~W~G~----a~~af~~~~~~~~~~~~~~~~~L~ 68 (86)
T PF06013_consen 20 ADELQSQLQQLESSIDSL--QASWQGE----AADAFQDKFEEWNQAFRQLNEALE 68 (86)
T ss_dssp HHHHHHHHHHHHHHHHHH--GGGBTSS----TSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH--hhhCCch----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555665555555555 1122333 335577888888766665555443
No 16
>COG3130 Rmf Ribosome modulation factor [Translation, ribosomal structure and biogenesis]
Probab=33.07 E-value=16 Score=27.32 Aligned_cols=12 Identities=33% Similarity=1.057 Sum_probs=9.7
Q ss_pred hhhhhcCCchhH
Q 020973 158 ALYWIGDWRPSA 169 (319)
Q Consensus 158 ~FLWiGGfRPS~ 169 (319)
--.|+||||--.
T Consensus 37 Rs~WLgGWRea~ 48 (55)
T COG3130 37 RSQWLGGWREAM 48 (55)
T ss_pred HHHHHHHHHHHh
Confidence 378999999654
No 17
>PHA02414 hypothetical protein
Probab=32.95 E-value=1.3e+02 Score=25.41 Aligned_cols=44 Identities=25% Similarity=0.487 Sum_probs=32.6
Q ss_pred cchhHHHHHHHHHHHHHhhhccccCCccccchhhhHHHHHHHHHHHhhhHHHHHHhccc
Q 020973 53 GEIDNIVERVENIVERVQCTTIHKSESSKRGEDISREKYSHWRQEQKTRAVSLEKQLNS 111 (319)
Q Consensus 53 ~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~ge~ls~~~Y~~W~eeq~r~l~eLr~Al~s 111 (319)
-+|.|++-|++.||-++|.+.. +..|+. .+++.-+.|||.-..+
T Consensus 4 ~~in~Lv~~v~~ledKiQ~Gel-----t~kgdn----------~eL~~av~ELRdivvs 47 (111)
T PHA02414 4 KEINNLVSQVETLEDKIQEGEL-----TDKGDN----------KELEVAVAELRDIVVS 47 (111)
T ss_pred hHHHHHHHHHHHHHHHHhcCcc-----ccCCch----------HHHHHHHHHHHHHHHH
Confidence 4789999999999999997554 555532 4666777777776654
No 18
>PF11459 DUF2893: Protein of unknwon function (DUF2893); InterPro: IPR021561 This is a bacterial family of uncharacterised proteins.
Probab=32.35 E-value=1.1e+02 Score=24.00 Aligned_cols=41 Identities=10% Similarity=0.268 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHH
Q 020973 251 KKIERVIIKAQQLRLKALELVVKKVLSPTDAAKFFVAFERIQ 292 (319)
Q Consensus 251 ~~Le~~l~qAD~LR~~TL~~lv~~ILTp~QAA~fLlA~~e~~ 292 (319)
+....++.-..+||-+.|+.+. +--|-.++.|-++.+|+.+
T Consensus 21 e~a~~l~egL~nLrp~~lq~LL-~~C~svKvkRLfl~lA~~~ 61 (69)
T PF11459_consen 21 EEADELMEGLRNLRPRVLQELL-EHCTSVKVKRLFLYLAERA 61 (69)
T ss_pred HHHHHHHHHHhhcCHHHHHHHH-HHCccHHHHHHHHHHHHHc
Confidence 3445667777789999999999 9999999999999999876
No 19
>PF04210 MtrG: Tetrahydromethanopterin S-methyltransferase, subunit G ; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=31.00 E-value=37 Score=26.82 Aligned_cols=24 Identities=29% Similarity=0.608 Sum_probs=21.4
Q ss_pred cccchhHHHHHHHHHHHHHhhhcc
Q 020973 51 DAGEIDNIVERVENIVERVQCTTI 74 (319)
Q Consensus 51 ~~~~~~~~~~~~~~~~~~~q~~~~ 74 (319)
+..+|..|.+||..|||+|-++.+
T Consensus 10 ~~~~~~~i~~rLd~iEeKvEf~~~ 33 (70)
T PF04210_consen 10 DPDDFNEIMKRLDEIEEKVEFTNA 33 (70)
T ss_pred CHHHHHHHHHHHHHHHHHHHhHHH
Confidence 557899999999999999998876
No 20
>PRK14563 ribosome modulation factor; Provisional
Probab=30.66 E-value=13 Score=28.12 Aligned_cols=15 Identities=27% Similarity=0.787 Sum_probs=10.6
Q ss_pred ChhhhhhhhhhcCCchh
Q 020973 152 PPHELAALYWIGDWRPS 168 (319)
Q Consensus 152 tplEra~FLWiGGfRPS 168 (319)
++.-| -.||||||-.
T Consensus 33 ~~~~r--~~Wl~GWReg 47 (55)
T PRK14563 33 TLDAR--SQWLGGWREA 47 (55)
T ss_pred CcHHH--HHHHHHHHHH
Confidence 44455 3899999954
No 21
>PF00589 Phage_integrase: Phage integrase family; InterPro: IPR002104 Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The catalytic site residues in CRE recombinase (P06956 from SWISSPROT) are Arg-173, His-289, Arg-292 and Tyr-324.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration; PDB: 1A0P_A 1Z1G_B 1Z19_A 1AE9_A 1Z1B_A 1P7D_B 2A3V_C 1Q3V_E 1Q3U_A 1OUQ_F ....
Probab=26.80 E-value=26 Score=28.72 Aligned_cols=21 Identities=33% Similarity=0.351 Sum_probs=14.5
Q ss_pred hhhhhcCCchhHHHHHHhhhc
Q 020973 158 ALYWIGDWRPSAILDLARGLV 178 (319)
Q Consensus 158 ~FLWiGGfRPS~llkLL~sl~ 178 (319)
.+++.+|+||++++.|=..-+
T Consensus 28 ~l~~~tG~R~~El~~l~~~~v 48 (173)
T PF00589_consen 28 LLLLYTGLRPSELLRLRWDDV 48 (173)
T ss_dssp HHHHHHT--HHHHHT-BGGGE
T ss_pred HHHHHHccchhhhhhhhhhhh
Confidence 478889999999999877643
No 22
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=25.26 E-value=30 Score=27.04 Aligned_cols=19 Identities=16% Similarity=0.244 Sum_probs=15.3
Q ss_pred CCCCChhhhhhhhhhcCCch
Q 020973 148 PRWTPPHELAALYWIGDWRP 167 (319)
Q Consensus 148 p~W~tplEra~FLWiGGfRP 167 (319)
.+.+.-.|| +|-||.+||-
T Consensus 44 ~~~Rw~VEr-~f~wlk~~Rr 62 (88)
T PF13586_consen 44 YKRRWVVER-TFAWLKRFRR 62 (88)
T ss_pred hccceehhh-hhHHHHHcCc
Confidence 445556999 9999999984
Done!