Query 030235
Match_columns 181
No_of_seqs 54 out of 56
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 10:38:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030235.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030235hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2608 CopZ Copper chaperone 99.0 9.2E-10 2E-14 77.0 6.4 65 99-169 3-70 (71)
2 PF00403 HMA: Heavy-metal-asso 98.9 1.1E-09 2.4E-14 72.1 4.1 58 102-165 2-62 (62)
3 KOG4656 Copper chaperone for s 97.3 0.00028 6.1E-09 61.7 4.5 63 97-166 6-68 (247)
4 PRK10671 copA copper exporting 97.0 0.0016 3.4E-08 62.6 6.6 63 99-169 4-66 (834)
5 KOG1603 Copper chaperone [Inor 96.9 0.0024 5.3E-08 44.6 5.3 54 110-169 16-70 (73)
6 PLN02957 copper, zinc superoxi 96.1 0.021 4.5E-07 48.1 6.8 63 100-169 8-70 (238)
7 KOG0207 Cation transport ATPas 95.9 0.0092 2E-07 60.3 4.7 54 110-169 6-61 (951)
8 TIGR00003 copper ion binding p 95.6 0.072 1.6E-06 30.5 5.8 62 99-166 3-67 (68)
9 KOG0207 Cation transport ATPas 93.3 0.16 3.6E-06 51.7 5.9 63 98-166 146-211 (951)
10 COG2217 ZntA Cation transport 92.2 0.23 5E-06 48.8 5.1 62 101-168 5-69 (713)
11 PRK10671 copA copper exporting 88.7 1.3 2.8E-05 43.1 6.7 63 99-167 100-162 (834)
12 TIGR00268 conserved hypothetic 87.8 0.92 2E-05 37.9 4.5 58 113-172 187-247 (252)
13 PRK11033 zntA zinc/cadmium/mer 80.8 5.2 0.00011 38.9 6.8 67 97-168 52-118 (741)
14 PF02120 Flg_hook: Flagellar h 80.2 2.9 6.2E-05 28.8 3.6 52 125-176 25-81 (85)
15 PF01883 DUF59: Domain of unkn 70.0 4 8.7E-05 27.7 2.2 22 110-131 51-72 (72)
16 PF02680 DUF211: Uncharacteriz 67.5 11 0.00025 29.2 4.4 54 109-168 15-76 (95)
17 PF13732 DUF4162: Domain of un 64.8 24 0.00051 24.1 5.2 44 120-171 26-71 (84)
18 PF03780 Asp23: Asp23 family; 64.1 12 0.00026 26.8 3.8 49 127-175 48-106 (108)
19 PF01709 Transcrip_reg: Transc 62.0 15 0.00032 31.4 4.6 49 115-173 148-197 (234)
20 COG0217 Uncharacterized conser 61.3 7.9 0.00017 34.3 2.9 68 94-171 126-199 (241)
21 PF11210 DUF2996: Protein of u 56.3 6.9 0.00015 31.6 1.5 30 108-138 11-40 (119)
22 COG1888 Uncharacterized protei 53.9 35 0.00075 26.9 5.0 56 107-168 15-78 (97)
23 cd04888 ACT_PheB-BS C-terminal 53.4 27 0.00059 22.8 3.8 36 96-131 39-74 (76)
24 COG2151 PaaD Predicted metal-s 53.3 11 0.00024 29.5 2.2 36 99-134 54-90 (111)
25 cd04909 ACT_PDH-BS C-terminal 52.1 49 0.0011 21.5 4.9 51 109-166 11-69 (69)
26 PF08262 Lem_TRP: Leucophaea m 50.7 5.9 0.00013 20.0 0.2 7 51-57 4-10 (10)
27 TIGR02945 SUF_assoc FeS assemb 50.1 16 0.00035 26.3 2.5 23 112-134 56-78 (99)
28 PF09580 Spore_YhcN_YlaJ: Spor 49.3 61 0.0013 25.4 5.8 52 110-161 74-128 (177)
29 PF08002 DUF1697: Protein of u 47.5 21 0.00045 28.0 2.9 60 113-175 21-81 (137)
30 TIGR02990 ectoine_eutA ectoine 46.7 27 0.00058 29.9 3.7 51 111-177 106-160 (239)
31 PRK00110 hypothetical protein; 46.2 30 0.00064 30.2 4.0 68 97-174 129-200 (245)
32 PRK11670 antiporter inner memb 42.7 46 0.001 29.9 4.7 52 111-167 65-140 (369)
33 PRK09577 multidrug efflux prot 41.4 52 0.0011 33.4 5.3 54 113-166 158-213 (1032)
34 TIGR03406 FeS_long_SufT probab 40.5 27 0.00058 29.0 2.7 38 98-135 117-155 (174)
35 TIGR02544 III_secr_YscJ type I 40.5 38 0.00081 28.2 3.6 54 115-168 111-182 (193)
36 TIGR02159 PA_CoA_Oxy4 phenylac 39.6 52 0.0011 26.5 4.1 51 122-174 13-67 (146)
37 PRK00435 ef1B elongation facto 39.3 55 0.0012 24.7 4.0 38 93-132 46-83 (88)
38 PF03927 NapD: NapD protein; 38.6 1.2E+02 0.0026 21.9 5.5 30 110-140 14-43 (79)
39 PF06345 Drf_DAD: DRF Autoregu 36.7 28 0.00061 19.3 1.5 12 150-161 1-12 (15)
40 PF03698 UPF0180: Uncharacteri 36.6 26 0.00056 26.2 1.8 18 153-170 11-28 (80)
41 cd04886 ACT_ThrD-II-like C-ter 35.5 1.1E+02 0.0024 18.9 5.9 59 109-167 8-72 (73)
42 cd04883 ACT_AcuB C-terminal AC 35.4 1.2E+02 0.0027 19.5 5.9 52 110-168 12-70 (72)
43 COG2092 EFB1 Translation elong 33.4 36 0.00078 26.2 2.2 23 110-132 61-83 (88)
44 cd04874 ACT_Af1403 N-terminal 33.3 1.1E+02 0.0024 19.0 4.2 32 97-131 40-71 (72)
45 PRK15124 2'-5' RNA ligase; Pro 32.6 1.4E+02 0.003 23.6 5.5 71 96-167 40-118 (176)
46 PF13399 LytR_C: LytR cell env 31.6 41 0.0009 23.5 2.2 20 149-168 15-34 (90)
47 TIGR02830 spore_III_AG stage I 30.3 43 0.00093 28.4 2.4 28 113-140 63-92 (186)
48 TIGR02898 spore_YhcN_YlaJ spor 30.1 1.5E+02 0.0033 24.3 5.5 29 112-140 55-83 (158)
49 PRK03094 hypothetical protein; 28.7 43 0.00093 25.2 1.9 19 153-171 11-29 (80)
50 PLN02633 palmitoyl protein thi 28.3 1.3E+02 0.0028 27.7 5.2 80 90-169 20-101 (314)
51 TIGR00489 aEF-1_beta translati 27.8 63 0.0014 24.3 2.7 38 93-132 46-83 (88)
52 PRK10555 aminoglycoside/multid 25.3 1.8E+02 0.0038 29.8 6.0 49 114-162 160-210 (1037)
53 COG1606 ATP-utilizing enzymes 25.3 1E+02 0.0022 28.0 4.0 54 118-172 198-253 (269)
54 PRK12378 hypothetical protein; 25.2 71 0.0015 27.7 2.9 70 97-174 126-199 (235)
55 COG1094 Predicted RNA-binding 24.5 69 0.0015 27.7 2.6 53 113-167 26-81 (194)
56 PRK10614 multidrug efflux syst 24.5 1.4E+02 0.003 30.4 5.1 53 108-162 59-115 (1025)
57 PF05430 Methyltransf_30: S-ad 24.5 47 0.001 25.9 1.5 18 152-169 92-109 (124)
58 PRK11026 ftsX cell division AB 23.9 69 0.0015 28.2 2.6 32 98-131 68-99 (309)
59 PF00564 PB1: PB1 domain; Int 23.5 90 0.002 21.1 2.6 47 128-180 3-53 (84)
60 PRK15368 pathogenicity island 23.1 88 0.0019 25.7 2.9 50 91-140 36-85 (127)
61 cd04882 ACT_Bt0572_2 C-termina 22.5 68 0.0015 20.1 1.8 52 110-166 10-64 (65)
62 PF01514 YscJ_FliF: Secretory 22.5 80 0.0017 26.3 2.6 52 115-166 119-188 (206)
63 PRK13558 bacterio-opsin activa 22.3 4.3E+02 0.0093 24.4 7.5 63 96-168 485-548 (665)
64 PF04972 BON: BON domain; Int 22.3 1.6E+02 0.0034 19.1 3.5 29 115-144 3-34 (64)
65 TIGR00325 lpxC UDP-3-0-acyl N- 21.8 1.7E+02 0.0036 26.6 4.6 50 111-168 73-122 (297)
66 TIGR00439 ftsX putative protei 21.5 82 0.0018 27.7 2.6 32 98-131 68-99 (309)
67 TIGR01033 DNA-binding regulato 21.2 1.3E+02 0.0028 26.0 3.7 68 97-174 129-202 (238)
68 cd04906 ACT_ThrD-I_1 First of 20.5 2.9E+02 0.0064 19.3 4.8 53 110-169 12-72 (85)
69 cd04903 ACT_LSD C-terminal ACT 20.4 2.2E+02 0.0049 17.5 3.9 29 99-131 42-70 (71)
70 PRK13187 UDP-3-O-[3-hydroxymyr 20.2 1.9E+02 0.004 26.4 4.6 63 97-168 72-135 (304)
71 PRK10598 lipoprotein; Provisio 20.1 52 0.0011 28.0 1.0 51 122-174 47-99 (186)
72 PF00736 EF1_GNE: EF-1 guanine 20.1 2.5E+02 0.0053 20.9 4.5 39 93-133 46-85 (89)
No 1
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.01 E-value=9.2e-10 Score=76.99 Aligned_cols=65 Identities=22% Similarity=0.510 Sum_probs=57.5
Q ss_pred EEEEeeccCCCCCchHHHHHHhccCCCceeeEEEEecceEEE---eeeccccccchHHHHHHHHHhCCccceee
Q 030235 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATV---EKQTTVQATGVAANLVEIIQGSGFKLQTL 169 (181)
Q Consensus 99 ~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV---~kqttvqatgvassLvEAIe~aGFevqtl 169 (181)
.+.|+-+|-==++|+.+|+++|+.++||.+|+|+|+.|.+.| ...++. ..|+++|+++||++...
T Consensus 3 ~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~------~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 3 KTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDI------EAIIEAIEDAGYKVEEI 70 (71)
T ss_pred eEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCH------HHHHHHHHHcCCCeeec
Confidence 356888888889999999999999999999999999988887 446784 99999999999998653
No 2
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=98.93 E-value=1.1e-09 Score=72.08 Aligned_cols=58 Identities=26% Similarity=0.465 Sum_probs=51.5
Q ss_pred EeeccCCCCCchHHHHHHhccCCCceeeEEEEecceEEE---eeeccccccchHHHHHHHHHhCCcc
Q 030235 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATV---EKQTTVQATGVAANLVEIIQGSGFK 165 (181)
Q Consensus 102 f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV---~kqttvqatgvassLvEAIe~aGFe 165 (181)
|+=+|-.-++|..+|+++|..++||.+++|++..+.++| +..+++ +.|+++|+++||+
T Consensus 2 ~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~------~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 2 FKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSI------EKIIEAIEKAGYE 62 (62)
T ss_dssp EEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCH------HHHHHHHHHTTSE
T ss_pred EEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCH------HHHHHHHHHhCcC
Confidence 555677788999999999999999999999999999999 334664 9999999999996
No 3
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=97.32 E-value=0.00028 Score=61.74 Aligned_cols=63 Identities=21% Similarity=0.363 Sum_probs=49.5
Q ss_pred ceEEEEeeccCCCCCchHHHHHHhccCCCceeeEEEEecceEEEeeeccccccchHHHHHHHHHhCCccc
Q 030235 97 KLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVEKQTTVQATGVAANLVEIIQGSGFKL 166 (181)
Q Consensus 97 ~l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV~kqttvqatgvassLvEAIe~aGFev 166 (181)
.+..-|--.=+ -|+||..|++.|++++||.+|+|+|+++.++|..+..+ ++|..+|+.-|=++
T Consensus 6 ~~~~efaV~M~-cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~------s~i~~~le~tGr~A 68 (247)
T KOG4656|consen 6 TYEAEFAVQMT-CESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPP------SEIQNTLENTGRDA 68 (247)
T ss_pred ceeEEEEEech-hHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCCh------HHHHHHHHhhChhe
Confidence 34444433333 68999999999999999999999999999999556664 78888888877654
No 4
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.00 E-value=0.0016 Score=62.62 Aligned_cols=63 Identities=19% Similarity=0.316 Sum_probs=52.5
Q ss_pred EEEEeeccCCCCCchHHHHHHhccCCCceeeEEEEecceEEEeeeccccccchHHHHHHHHHhCCccceee
Q 030235 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVEKQTTVQATGVAANLVEIIQGSGFKLQTL 169 (181)
Q Consensus 99 ~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV~kqttvqatgvassLvEAIe~aGFevqtl 169 (181)
+.-|+-+|---++|+.+|+++|+.++||.+++|++. .+++....+. ..|+++|+++||++..+
T Consensus 4 ~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~------~~i~~~i~~~Gy~~~~~ 66 (834)
T PRK10671 4 TIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASA------EALIETIKQAGYDASVS 66 (834)
T ss_pred EEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCH------HHHHHHHHhcCCccccc
Confidence 355777888889999999999999999999999995 4455334453 89999999999999864
No 5
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=96.92 E-value=0.0024 Score=44.64 Aligned_cols=54 Identities=17% Similarity=0.294 Sum_probs=47.3
Q ss_pred CCchHHHHHHhccCCCceeeEEEEecceEEEeeeccccccchHHHHHHHHHhCC-ccceee
Q 030235 110 ETAIPAVTQALQGTEGISDLKVQVIEGIATVEKQTTVQATGVAANLVEIIQGSG-FKLQTL 169 (181)
Q Consensus 110 e~cV~sVTkALE~leGVsdVkVsLeeG~AtV~kqttvqatgvassLvEAIe~aG-Fevqtl 169 (181)
++|..+|.++|..++||.++++++.++..+|....++ +.|.+.|++.| .+...+
T Consensus 16 ~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p------~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 16 EGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDP------VKLLKKLKKTGGKRAELW 70 (73)
T ss_pred ccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCH------HHHHHHHHhcCCCceEEe
Confidence 6899999999999999999999999999999555885 89999999887 665443
No 6
>PLN02957 copper, zinc superoxide dismutase
Probab=96.11 E-value=0.021 Score=48.06 Aligned_cols=63 Identities=17% Similarity=0.289 Sum_probs=51.2
Q ss_pred EEEeeccCCCCCchHHHHHHhccCCCceeeEEEEecceEEEeeeccccccchHHHHHHHHHhCCccceee
Q 030235 100 MYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVEKQTTVQATGVAANLVEIIQGSGFKLQTL 169 (181)
Q Consensus 100 m~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV~kqttvqatgvassLvEAIe~aGFevqtl 169 (181)
+.|.. |---+.|+.+|+++|..++||..+.+++..+.+.|....+ .+.|+++|++.||++.-+
T Consensus 8 ~~~~V-gMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~------~~~I~~aIe~~Gy~a~~~ 70 (238)
T PLN02957 8 TEFMV-DMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSP------VKAMTAALEQTGRKARLI 70 (238)
T ss_pred EEEEE-CccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCC------HHHHHHHHHHcCCcEEEe
Confidence 44555 5335799999999999999999999999999998843344 478999999999997544
No 7
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=95.95 E-value=0.0092 Score=60.32 Aligned_cols=54 Identities=19% Similarity=0.365 Sum_probs=49.6
Q ss_pred CCchHHHHHHhccCCCceeeEEEEecceEEE--eeeccccccchHHHHHHHHHhCCccceee
Q 030235 110 ETAIPAVTQALQGTEGISDLKVQVIEGIATV--EKQTTVQATGVAANLVEIIQGSGFKLQTL 169 (181)
Q Consensus 110 e~cV~sVTkALE~leGVsdVkVsLeeG~AtV--~kqttvqatgvassLvEAIe~aGFevqtl 169 (181)
-.|+.++.+++...+||.++.|+|..+.++| ...+++ +.|+|+|+|+||+..-+
T Consensus 6 ~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~------~~i~~~ied~gf~~~~~ 61 (951)
T KOG0207|consen 6 SACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSP------ESIKETIEDMGFEASLL 61 (951)
T ss_pred HHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCH------HHHHHHhhcccceeeec
Confidence 4699999999999999999999999999999 888885 99999999999998654
No 8
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=95.61 E-value=0.072 Score=30.45 Aligned_cols=62 Identities=19% Similarity=0.318 Sum_probs=48.7
Q ss_pred EEEEeeccCCCCCchHHHHHHhccCCCceeeEEEEecceEEEe---eeccccccchHHHHHHHHHhCCccc
Q 030235 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVE---KQTTVQATGVAANLVEIIQGSGFKL 166 (181)
Q Consensus 99 ~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV~---kqttvqatgvassLvEAIe~aGFev 166 (181)
.+.|.-+|---..|...+++.+...+|+..+.+++..+...+. ...+ ...+...+.+.||.+
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQAT------EICIAEAILDAGYEV 67 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCC------HHHHHHHHHHcCCCc
Confidence 3456667766679999999999999999999999999988772 2233 366777889999975
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=93.34 E-value=0.16 Score=51.69 Aligned_cols=63 Identities=17% Similarity=0.374 Sum_probs=57.6
Q ss_pred eEEEEeeccCCCCCchHHHHHHhccCCCceeeEEEEecceEEE---eeeccccccchHHHHHHHHHhCCccc
Q 030235 98 LTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATV---EKQTTVQATGVAANLVEIIQGSGFKL 166 (181)
Q Consensus 98 l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV---~kqttvqatgvassLvEAIe~aGFev 166 (181)
=..+|.-.|-+...|+.+|.+.|+.++||.+.+|++..+.+.| +.-+.+ -.+.++|+..||+.
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~p------r~i~k~ie~~~~~~ 211 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGP------RDIIKAIEETGFEA 211 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccCh------HHHHHHHHhhcccc
Confidence 3678999999999999999999999999999999999999999 666665 88999999999994
No 10
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=92.24 E-value=0.23 Score=48.81 Aligned_cols=62 Identities=18% Similarity=0.368 Sum_probs=52.5
Q ss_pred EEeeccCCCCCchHHHHHHhccCCCceeeEEEEecceEEE---eeeccccccchHHHHHHHHHhCCcccee
Q 030235 101 YFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATV---EKQTTVQATGVAANLVEIIQGSGFKLQT 168 (181)
Q Consensus 101 ~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV---~kqttvqatgvassLvEAIe~aGFevqt 168 (181)
.|+=+|--...|+..|+ +|+.++||.++.|++....+.| ....+. .+.+..+|++.||....
T Consensus 5 ~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~-----~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 5 SLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDL-----PADIVAAVEKAGYSARL 69 (713)
T ss_pred EEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEeccccccc-----HHHHHHHHHhcCccccc
Confidence 35667878889999999 9999999999999999999999 223341 48999999999998765
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=88.67 E-value=1.3 Score=43.09 Aligned_cols=63 Identities=21% Similarity=0.372 Sum_probs=54.4
Q ss_pred EEEEeeccCCCCCchHHHHHHhccCCCceeeEEEEecceEEEeeeccccccchHHHHHHHHHhCCccce
Q 030235 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVEKQTTVQATGVAANLVEIIQGSGFKLQ 167 (181)
Q Consensus 99 ~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV~kqttvqatgvassLvEAIe~aGFevq 167 (181)
++.|.-+|.--..|...+.+.|+.++||.+++|++..+.+.+....+ .+.+.+.+++.||...
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s------~~~I~~~I~~~Gy~a~ 162 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSAS------PQDLVQAVEKAGYGAE 162 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCC------HHHHHHHHHhcCCCcc
Confidence 67888999999999999999999999999999999999888843344 3678889999999864
No 12
>TIGR00268 conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.
Probab=87.83 E-value=0.92 Score=37.95 Aligned_cols=58 Identities=16% Similarity=0.393 Sum_probs=45.0
Q ss_pred hHHHHHHhccCCCceeeEEEEecceEEE---eeeccccccchHHHHHHHHHhCCccceeeccc
Q 030235 113 IPAVTQALQGTEGISDLKVQVIEGIATV---EKQTTVQATGVAANLVEIIQGSGFKLQTLNLS 172 (181)
Q Consensus 113 V~sVTkALE~leGVsdVkVsLeeG~AtV---~kqttvqatgvassLvEAIe~aGFevqtl~ls 172 (181)
|....+.|..+ |.++++|...++.|++ ++... ++..-...|...+...||+-.+|.|.
T Consensus 187 v~~~E~~l~~~-g~~~~rvr~~~~~a~ie~~~~~~~-~~~~~~~~i~~~~~~~gf~~v~ldl~ 247 (252)
T TIGR00268 187 VDEAEEVLRNA-GVGQVRVRNYDNLAVIEVPEDELS-KLLNEAEEVRDKFKDIGFRKVLIDLE 247 (252)
T ss_pred HHHHHHHHHHc-CCCeEEEEecCCeEEEEECHHHHH-HHHhhHHHHHHHHHHcCCCeEEEccC
Confidence 66777889997 9999999999999999 22222 11111477999999999999999874
No 13
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=80.77 E-value=5.2 Score=38.95 Aligned_cols=67 Identities=16% Similarity=0.288 Sum_probs=51.4
Q ss_pred ceEEEEeeccCCCCCchHHHHHHhccCCCceeeEEEEecceEEEeeeccccccchHHHHHHHHHhCCcccee
Q 030235 97 KLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVEKQTTVQATGVAANLVEIIQGSGFKLQT 168 (181)
Q Consensus 97 ~l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV~kqttvqatgvassLvEAIe~aGFevqt 168 (181)
.=...|+-+|---..|...++++|+.++||.+++|++..+.+.+.-..+. .+.+.+++++.||++..
T Consensus 52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~-----~~~I~~aI~~~Gy~a~~ 118 (741)
T PRK11033 52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDI-----RAQVESAVQKAGFSLRD 118 (741)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccc-----hHHHHHHHHhccccccc
Confidence 33455666666668999999999999999999999999888777221111 26778899999998754
No 14
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=80.23 E-value=2.9 Score=28.83 Aligned_cols=52 Identities=21% Similarity=0.292 Sum_probs=34.1
Q ss_pred CceeeEEEEecceEEE-----eeeccccccchHHHHHHHHHhCCccceeecccccCc
Q 030235 125 GISDLKVQVIEGIATV-----EKQTTVQATGVAANLVEIIQGSGFKLQTLNLSFDDE 176 (181)
Q Consensus 125 GVsdVkVsLeeG~AtV-----~kqttvqatgvassLvEAIe~aGFevqtl~lsf~d~ 176 (181)
|=-+|++.+.++..++ ...+--..-.-...|+++++..||++..++.+..+.
T Consensus 25 G~v~v~l~~~~~~l~v~~~~~~~~~~~~L~~~~~~L~~~L~~~G~~~~~~~v~~~~~ 81 (85)
T PF02120_consen 25 GSVEVKLRLQGGNLSVQFTAENPETKELLRQNLPELKERLQAQGLEVVNLSVSQGSS 81 (85)
T ss_dssp --EEEEEEEETTEEEEEEE--SSHHHHHHHHTHHHHHHHHHTTT-EEEEEEEESS--
T ss_pred CcEEEEEEEeCCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCeEEEEEEECCC
Confidence 3347888899998777 112222223446789999999999999988876554
No 15
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=69.97 E-value=4 Score=27.68 Aligned_cols=22 Identities=27% Similarity=0.448 Sum_probs=17.5
Q ss_pred CCchHHHHHHhccCCCceeeEE
Q 030235 110 ETAIPAVTQALQGTEGISDLKV 131 (181)
Q Consensus 110 e~cV~sVTkALE~leGVsdVkV 131 (181)
+.--..++++|.+++||++|+|
T Consensus 51 ~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 51 EPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHHHHhCCCCceEeC
Confidence 3345789999999999999987
No 16
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=67.51 E-value=11 Score=29.24 Aligned_cols=54 Identities=22% Similarity=0.346 Sum_probs=39.4
Q ss_pred CCCchHHHHHHhccCCCceeeEEEEecc-------eEEE-eeeccccccchHHHHHHHHHhCCcccee
Q 030235 109 NETAIPAVTQALQGTEGISDLKVQVIEG-------IATV-EKQTTVQATGVAANLVEIIQGSGFKLQT 168 (181)
Q Consensus 109 ~e~cV~sVTkALE~leGVsdVkVsLeeG-------~AtV-~kqttvqatgvassLvEAIe~aGFevqt 168 (181)
.+..+.-+.++|..++||..|++++.+= ..++ -...+ -+.|+++|++.|=-++.
T Consensus 15 ~~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id------~d~i~~~Ie~~Gg~IHS 76 (95)
T PF02680_consen 15 HEPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDID------FDEIKEAIEELGGVIHS 76 (95)
T ss_dssp SSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-------HHHHHHHHHHTT-EEEE
T ss_pred CCCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCC------HHHHHHHHHHcCCeEEe
Confidence 4667888999999999999999988652 1222 44567 49999999999965554
No 17
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=64.81 E-value=24 Score=24.08 Aligned_cols=44 Identities=18% Similarity=0.351 Sum_probs=33.4
Q ss_pred hccCCCceeeEEEEecceEEE--eeeccccccchHHHHHHHHHhCCccceeecc
Q 030235 120 LQGTEGISDLKVQVIEGIATV--EKQTTVQATGVAANLVEIIQGSGFKLQTLNL 171 (181)
Q Consensus 120 LE~leGVsdVkVsLeeG~AtV--~kqttvqatgvassLvEAIe~aGFevqtl~l 171 (181)
|+.++||.+++- ..+|..++ ....+ +..|.+.+.+.|+ +..++.
T Consensus 26 l~~~~~v~~v~~-~~~~~~~i~l~~~~~------~~~ll~~l~~~g~-I~~f~~ 71 (84)
T PF13732_consen 26 LEELPGVESVEQ-DGDGKLRIKLEDEET------ANELLQELIEKGI-IRSFEE 71 (84)
T ss_pred HhhCCCeEEEEE-eCCcEEEEEECCccc------HHHHHHHHHhCCC-eeEEEE
Confidence 888999999974 35665777 44444 5889999999999 876654
No 18
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=64.14 E-value=12 Score=26.85 Aligned_cols=49 Identities=24% Similarity=0.399 Sum_probs=29.5
Q ss_pred eeeEEEEe-cceEEE------eeeccc--cccchHHHHHHHHHhC-CccceeecccccC
Q 030235 127 SDLKVQVI-EGIATV------EKQTTV--QATGVAANLVEIIQGS-GFKLQTLNLSFDD 175 (181)
Q Consensus 127 sdVkVsLe-eG~AtV------~kqttv--qatgvassLvEAIe~a-GFevqtl~lsf~d 175 (181)
..++|... ++...| .-..++ -+.-+...++++|+.. |+++...|..++|
T Consensus 48 ~~v~v~~~~~~~i~v~l~v~v~~g~~i~~v~~~iq~~V~~~v~~~tg~~v~~V~V~V~~ 106 (108)
T PF03780_consen 48 KGVKVEVDEDGGITVDLHVVVEYGVNIPEVAEEIQEKVKEAVEEMTGIEVSEVNVHVED 106 (108)
T ss_pred CCeEEEEccCcceEEEEEEEEECCccHHHHHHHHHHHHHHHHHHHHCCeeEEEEEEEEe
Confidence 34677777 777666 112222 1223445556666664 9999999887765
No 19
>PF01709 Transcrip_reg: Transcriptional regulator; InterPro: IPR002876 This entry represents the core region of several hypothetical proteins found in bacteria, plants, and yeast proteins. This core region can be subdivided into three domains: a 3-helical bundle domain, and two alpha+beta domains with different folds, where domain 3 (ferredoxin-like fold) is inserted within domain 2. This core region is found in the following hypothetical proteins: YebC from Escherichia coli, HP0162 from Helicobacter pylori (Campylobacter pylori) and aq1575 from Aquifex aeolicus []. The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined. A structural homology search reveals that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protein reveals a monomer consisting of three domains arranged along a pseudo threefold symmetry axis. There is a large cleft with approximate dimensions of 10 A x 10 A x 20 A in the centre of the three domains along the symmetry axis. Two possible active sites are suggested based on the structure and multiple sequence alignment. There are several highly conserved residues in these putative active sites [].; PDB: 1LFP_A 1MW7_A 1KON_A.
Probab=61.96 E-value=15 Score=31.42 Aligned_cols=49 Identities=12% Similarity=0.370 Sum_probs=36.6
Q ss_pred HHHHHhccCCCceeeEEEEecceEEE-eeeccccccchHHHHHHHHHhCCccceeecccc
Q 030235 115 AVTQALQGTEGISDLKVQVIEGIATV-EKQTTVQATGVAANLVEIIQGSGFKLQTLNLSF 173 (181)
Q Consensus 115 sVTkALE~leGVsdVkVsLeeG~AtV-~kqttvqatgvassLvEAIe~aGFevqtl~lsf 173 (181)
-+.-||+. |+.||+. ++|...| ..+.+. ..++++++..||++..-.+.|
T Consensus 148 ~~e~aIe~--GaeDve~--~d~~~~~~c~p~~~------~~v~~~L~~~g~~i~~~e~~~ 197 (234)
T PF01709_consen 148 LMEDAIEA--GAEDVEE--DDGEFEFICDPSDL------SAVKKALEKKGYEIESAELEY 197 (234)
T ss_dssp HHHHHHHH--TESEEEE--CTSEEEEEEEGGGH------HHHHHHHHHTT---SEEEEEE
T ss_pred HHHHHHhC--CCcEeee--cCCeEEEEECHHHH------HHHHHHHHHcCCCeeEEEEEE
Confidence 34557775 9999983 3788888 888885 999999999999998777765
No 20
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=61.28 E-value=7.9 Score=34.32 Aligned_cols=68 Identities=16% Similarity=0.390 Sum_probs=49.4
Q ss_pred CCcceEEEEeeccCCC--CC--c-hHHHHHHhccCCCceeeEEEEecceEEE-eeeccccccchHHHHHHHHHhCCccce
Q 030235 94 PSDKLTMYFQADGAMN--ET--A-IPAVTQALQGTEGISDLKVQVIEGIATV-EKQTTVQATGVAANLVEIIQGSGFKLQ 167 (181)
Q Consensus 94 ~sd~l~m~f~aegt~~--e~--c-V~sVTkALE~leGVsdVkVsLeeG~AtV-~kqttvqatgvassLvEAIe~aGFevq 167 (181)
++-++..+|..-|-+. .. - =.-...+||+ |+.||..+ +|...| +.+.+- ..++++++++||+..
T Consensus 126 ~~GSV~~mF~~kGvi~~~~~~~~ed~l~e~~iea--gaeDv~~~--~~~~~V~t~p~~~------~~V~~~L~~~g~~~~ 195 (241)
T COG0217 126 EPGSVSYMFDRKGVIVVEKNEIDEDELLEAAIEA--GAEDVEED--EGSIEVYTEPEDF------NKVKEALEAAGYEIE 195 (241)
T ss_pred CCceEEEEEeccEEEEECCCCCCHHHHHHHHHHC--CchhhhcC--CCeEEEEEChHHH------HHHHHHHHHcCCcee
Confidence 4456777888777542 22 1 2234566777 99999998 777888 889995 999999999999987
Q ss_pred eecc
Q 030235 168 TLNL 171 (181)
Q Consensus 168 tl~l 171 (181)
.--|
T Consensus 196 ~ael 199 (241)
T COG0217 196 SAEL 199 (241)
T ss_pred eeeE
Confidence 6333
No 21
>PF11210 DUF2996: Protein of unknown function (DUF2996); InterPro: IPR021374 This family of proteins has no known function.
Probab=56.33 E-value=6.9 Score=31.56 Aligned_cols=30 Identities=30% Similarity=0.519 Sum_probs=27.2
Q ss_pred CCCCchHHHHHHhccCCCceeeEEEEecceE
Q 030235 108 MNETAIPAVTQALQGTEGISDLKVQVIEGIA 138 (181)
Q Consensus 108 ~~e~cV~sVTkALE~leGVsdVkVsLeeG~A 138 (181)
|++.-+|+++++|++- ||+++++++.++.-
T Consensus 11 i~ed~lPaL~~~l~~~-Gi~d~~L~f~~~~~ 40 (119)
T PF11210_consen 11 IEEDFLPALKKALEKE-GISDVELSFEKNKR 40 (119)
T ss_pred HHHhhhHHHHHHHHHc-CCCcceEEeccCCc
Confidence 6788899999999998 99999999999943
No 22
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=53.92 E-value=35 Score=26.90 Aligned_cols=56 Identities=18% Similarity=0.246 Sum_probs=41.9
Q ss_pred CCCCCchHHHHHHhccCCCceeeEEEEecceE-------EE-eeeccccccchHHHHHHHHHhCCcccee
Q 030235 107 AMNETAIPAVTQALQGTEGISDLKVQVIEGIA-------TV-EKQTTVQATGVAANLVEIIQGSGFKLQT 168 (181)
Q Consensus 107 t~~e~cV~sVTkALE~leGVsdVkVsLeeG~A-------tV-~kqttvqatgvassLvEAIe~aGFevqt 168 (181)
-+++.-+.-+-+.|..++||.-|++.|.+=-. ++ -...+ -+.|++.|++.|=-++.
T Consensus 15 P~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ld------ydei~~~iE~~Gg~IHS 78 (97)
T COG1888 15 PHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLD------YDEIEEVIEELGGAIHS 78 (97)
T ss_pred CcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCC------HHHHHHHHHHcCCeeee
Confidence 45677888899999999999999888865322 22 34555 38999999999865543
No 23
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=53.39 E-value=27 Score=22.83 Aligned_cols=36 Identities=11% Similarity=0.290 Sum_probs=28.8
Q ss_pred cceEEEEeeccCCCCCchHHHHHHhccCCCceeeEE
Q 030235 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKV 131 (181)
Q Consensus 96 d~l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkV 131 (181)
....+.|--+-.-.+..+..+-+.|..++||.+|++
T Consensus 39 ~~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 39 GRANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred CeEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 346677776666556689999999999999999876
No 24
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=53.31 E-value=11 Score=29.48 Aligned_cols=36 Identities=25% Similarity=0.453 Sum_probs=26.0
Q ss_pred EEEEeeccC-CCCCchHHHHHHhccCCCceeeEEEEe
Q 030235 99 TMYFQADGA-MNETAIPAVTQALQGTEGISDLKVQVI 134 (181)
Q Consensus 99 ~m~f~aegt-~~e~cV~sVTkALE~leGVsdVkVsLe 134 (181)
.|-+.+.|= +++--...|+.+|++++||.+++|.|.
T Consensus 54 ~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l~ 90 (111)
T COG2151 54 KMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVELT 90 (111)
T ss_pred EEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEEE
Confidence 444444442 233346789999999999999999874
No 25
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=52.15 E-value=49 Score=21.54 Aligned_cols=51 Identities=27% Similarity=0.490 Sum_probs=32.1
Q ss_pred CCCchHHHHHHhccCCCc--eeeEEEEe----cceEEE--eeeccccccchHHHHHHHHHhCCccc
Q 030235 109 NETAIPAVTQALQGTEGI--SDLKVQVI----EGIATV--EKQTTVQATGVAANLVEIIQGSGFKL 166 (181)
Q Consensus 109 ~e~cV~sVTkALE~leGV--sdVkVsLe----eG~AtV--~kqttvqatgvassLvEAIe~aGFev 166 (181)
..|.+..+++.|.+- |+ .++...-. .+...+ .-+.+ .+.+++.++++||++
T Consensus 11 ~~G~L~~l~~~l~~~-~i~i~~~~~~~~~~~~~~~~~i~v~~~~~------~~~~~~~L~~~G~~v 69 (69)
T cd04909 11 EPGVIAEVTQILGDA-GISIKNIEILEIREGIGGILRISFKTQED------RERAKEILKEAGYEV 69 (69)
T ss_pred CCCHHHHHHHHHHHc-CCCceeeEeEEeecCCcEEEEEEECCHHH------HHHHHHHHHHcCCcC
Confidence 356788899999776 33 33333332 233333 21234 489999999999975
No 26
>PF08262 Lem_TRP: Leucophaea maderae tachykinin-related peptide ; InterPro: IPR013206 These peptides are designated Leucophaea maderae (Madeira cockroach) tachykinin-related peptides (Lem TRPs). Some were isolated from the midgut of L. maderae, whereas others appear to be brain specific. The Lem TRPs of the brain are myotropic and induce increases in the amplitude and frequency of spontaneous contractions and tonus of hindgut muscle in L. maderae []. They were also isolated from brain-corpora, cardiaca-corpora, allata-suboesophageal ganglion extracts of Locusta migratoria (Migratory locust). They stimulate visceral muscle contractions of the oviduct and the foregut of L. migratoria [].
Probab=50.74 E-value=5.9 Score=20.01 Aligned_cols=7 Identities=71% Similarity=1.398 Sum_probs=5.4
Q ss_pred cccccce
Q 030235 51 WGFNGMR 57 (181)
Q Consensus 51 ~~~~~~r 57 (181)
-||||+|
T Consensus 4 mgf~g~r 10 (10)
T PF08262_consen 4 MGFHGMR 10 (10)
T ss_pred ccccccC
Confidence 4789886
No 27
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=50.14 E-value=16 Score=26.27 Aligned_cols=23 Identities=17% Similarity=0.397 Sum_probs=20.1
Q ss_pred chHHHHHHhccCCCceeeEEEEe
Q 030235 112 AIPAVTQALQGTEGISDLKVQVI 134 (181)
Q Consensus 112 cV~sVTkALE~leGVsdVkVsLe 134 (181)
-...++.+|.+++|+.+|+|.+.
T Consensus 56 l~~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 56 MPGEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHHHhCCCCceEEEEEE
Confidence 45678999999999999999986
No 28
>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=49.29 E-value=61 Score=25.36 Aligned_cols=52 Identities=12% Similarity=0.196 Sum_probs=37.3
Q ss_pred CCchHHHHHHhccCCCceeeEEEEecceEEE---eeeccccccchHHHHHHHHHh
Q 030235 110 ETAIPAVTQALQGTEGISDLKVQVIEGIATV---EKQTTVQATGVAANLVEIIQG 161 (181)
Q Consensus 110 e~cV~sVTkALE~leGVsdVkVsLeeG~AtV---~kqttvqatgvassLvEAIe~ 161 (181)
..--..|.+.+..++||.++.|-+.+..|-| .+...-...-+...+.++++.
T Consensus 74 ~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~~~~~~~~~i~~~V~~~v~~ 128 (177)
T PF09580_consen 74 QQLADRIANRVKKVPGVEDATVVVTDDNAYVAVDLDFNRFNTKKIKKKVEKAVKS 128 (177)
T ss_pred HHHHHHHHHHHhcCCCceEEEEEEECCEEEEEEEecccccchhHHHHHHHHHHHH
Confidence 3445789999999999999999999999999 221123333445666666665
No 29
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=47.46 E-value=21 Score=28.04 Aligned_cols=60 Identities=17% Similarity=0.355 Sum_probs=38.6
Q ss_pred hHHHHHHhccCCCceeeEEEEecceEEEeeeccccccchHHHHHHHHH-hCCccceeecccccC
Q 030235 113 IPAVTQALQGTEGISDLKVQVIEGIATVEKQTTVQATGVAANLVEIIQ-GSGFKLQTLNLSFDD 175 (181)
Q Consensus 113 V~sVTkALE~leGVsdVkVsLeeG~AtV~kqttvqatgvassLvEAIe-~aGFevqtl~lsf~d 175 (181)
-+-++.+|+++ |-.+|+-.+..|++.+....+. ..++..|.++|+ ..||++..+-++-++
T Consensus 21 MaeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~--~~l~~~ie~~l~~~fG~~v~v~vrs~~e 81 (137)
T PF08002_consen 21 MAELREALEDL-GFTNVRTYIQSGNVVFESDRDP--AELAAKIEKALEERFGFDVPVIVRSAEE 81 (137)
T ss_dssp HHHHHHHHHHC-T-EEEEEETTTTEEEEEESS-H--HHHHHHHHHHHHHH-TT---EEEEEHHH
T ss_pred HHHHHHHHHHc-CCCCceEEEeeCCEEEecCCCh--HHHHHHHHHHHHHhcCCCeEEEEeeHHH
Confidence 35688999999 9999999999999999644442 334555555554 369988777665443
No 30
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=46.73 E-value=27 Score=29.85 Aligned_cols=51 Identities=18% Similarity=0.371 Sum_probs=36.9
Q ss_pred CchHHHHHHhccCCCceeeEEEEecceEEE---eeeccccccchHHHHHHHHHhCCccceee-cccccCcc
Q 030235 111 TAIPAVTQALQGTEGISDLKVQVIEGIATV---EKQTTVQATGVAANLVEIIQGSGFKLQTL-NLSFDDEE 177 (181)
Q Consensus 111 ~cV~sVTkALE~leGVsdVkVsLeeG~AtV---~kqttvqatgvassLvEAIe~aGFevqtl-~lsf~d~~ 177 (181)
+.+.++-.||+++ |++.+- -+ ...++ ..+++-++++||++... +|..+|+.
T Consensus 106 t~~~A~~~AL~al-g~~RIa--------lvTPY~~~v~-------~~~~~~l~~~G~eV~~~~~~~~~~~~ 160 (239)
T TIGR02990 106 TPSSAAVDGLAAL-GVRRIS--------LLTPYTPETS-------RPMAQYFAVRGFEIVNFTCLGLTDDR 160 (239)
T ss_pred CHHHHHHHHHHHc-CCCEEE--------EECCCcHHHH-------HHHHHHHHhCCcEEeeeeccCCCCCc
Confidence 4456777888888 777653 34 44444 89999999999999887 66665543
No 31
>PRK00110 hypothetical protein; Validated
Probab=46.25 E-value=30 Score=30.17 Aligned_cols=68 Identities=12% Similarity=0.249 Sum_probs=46.0
Q ss_pred ceEEEEeeccCCCCC--chH-HHHHHhccCCCceeeEEEEecceEEE-eeeccccccchHHHHHHHHHhCCccceeeccc
Q 030235 97 KLTMYFQADGAMNET--AIP-AVTQALQGTEGISDLKVQVIEGIATV-EKQTTVQATGVAANLVEIIQGSGFKLQTLNLS 172 (181)
Q Consensus 97 ~l~m~f~aegt~~e~--cV~-sVTkALE~leGVsdVkVsLeeG~AtV-~kqttvqatgvassLvEAIe~aGFevqtl~ls 172 (181)
....+|.--|.+.=. -.. -..-||++ |+.||+. ++|...| ..+.+. ..++++++..||++..-.+.
T Consensus 129 sv~~~Fe~kG~i~~~~~~~d~~~e~aiea--GaeDv~~--e~~~~~i~~~p~~~------~~v~~~L~~~g~~~~~sei~ 198 (245)
T PRK00110 129 SVSYMFDRKGVIVIEPLDEDELMEAALEA--GAEDVET--DDESFEVITAPEDF------EAVRDALEAAGLEAESAEVT 198 (245)
T ss_pred ceEEEeccceEEEeCCCCHHHHHHHHHhC--CCCEeec--cCCeEEEEECHHHH------HHHHHHHHHcCCCeeeeEEE
Confidence 455677766654321 122 23445653 8888754 6777777 888885 89999999999998777666
Q ss_pred cc
Q 030235 173 FD 174 (181)
Q Consensus 173 f~ 174 (181)
|-
T Consensus 199 ~~ 200 (245)
T PRK00110 199 MI 200 (245)
T ss_pred Ee
Confidence 64
No 32
>PRK11670 antiporter inner membrane protein; Provisional
Probab=42.66 E-value=46 Score=29.90 Aligned_cols=52 Identities=17% Similarity=0.219 Sum_probs=37.2
Q ss_pred CchHHHHHHhccCCCceeeEEEEecce---------------EE---E------eeeccccccchHHHHHHHHHhCCccc
Q 030235 111 TAIPAVTQALQGTEGISDLKVQVIEGI---------------AT---V------EKQTTVQATGVAANLVEIIQGSGFKL 166 (181)
Q Consensus 111 ~cV~sVTkALE~leGVsdVkVsLeeG~---------------At---V------~kqttvqatgvassLvEAIe~aGFev 166 (181)
.-...++++|.+++||++|+|.+.+.. .. | ..+++ ++..|--++...|+++
T Consensus 65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT-----~avNLA~aLA~~G~rV 139 (369)
T PRK11670 65 ELKEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSS-----TAVNLALALAAEGAKV 139 (369)
T ss_pred HHHHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHH-----HHHHHHHHHHHCCCcE
Confidence 345679999999999999999887631 11 1 22334 3778888888889988
Q ss_pred e
Q 030235 167 Q 167 (181)
Q Consensus 167 q 167 (181)
-
T Consensus 140 l 140 (369)
T PRK11670 140 G 140 (369)
T ss_pred E
Confidence 4
No 33
>PRK09577 multidrug efflux protein; Reviewed
Probab=41.37 E-value=52 Score=33.41 Aligned_cols=54 Identities=19% Similarity=0.299 Sum_probs=35.9
Q ss_pred hHHHHHHhccCCCceeeEEEEecceEEE-eeeccccccch-HHHHHHHHHhCCccc
Q 030235 113 IPAVTQALQGTEGISDLKVQVIEGIATV-EKQTTVQATGV-AANLVEIIQGSGFKL 166 (181)
Q Consensus 113 V~sVTkALE~leGVsdVkVsLeeG~AtV-~kqttvqatgv-assLvEAIe~aGFev 166 (181)
-..+...|+.++||.+|++.=.+-+..| ..+.-.++-|+ .+.+.++|+..+.+.
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n~~~ 213 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHNARV 213 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhCCcC
Confidence 4568899999999999998754444444 23322233443 377888888876654
No 34
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=40.52 E-value=27 Score=29.00 Aligned_cols=38 Identities=16% Similarity=0.361 Sum_probs=26.9
Q ss_pred eEEEEeecc-CCCCCchHHHHHHhccCCCceeeEEEEec
Q 030235 98 LTMYFQADG-AMNETAIPAVTQALQGTEGISDLKVQVIE 135 (181)
Q Consensus 98 l~m~f~aeg-t~~e~cV~sVTkALE~leGVsdVkVsLee 135 (181)
++|-+-+-| .|-+.....|+++|.+++||++|+|++.-
T Consensus 117 I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l~~ 155 (174)
T TIGR03406 117 IEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVELVF 155 (174)
T ss_pred EEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEEEe
Confidence 444444333 34445567799999999999999998753
No 35
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=40.48 E-value=38 Score=28.22 Aligned_cols=54 Identities=17% Similarity=0.269 Sum_probs=35.6
Q ss_pred HHHHHhccCCCceeeEEEEe------------cceEEE---ee---eccccccchHHHHHHHHHhCCcccee
Q 030235 115 AVTQALQGTEGISDLKVQVI------------EGIATV---EK---QTTVQATGVAANLVEIIQGSGFKLQT 168 (181)
Q Consensus 115 sVTkALE~leGVsdVkVsLe------------eG~AtV---~k---qttvqatgvassLvEAIe~aGFevqt 168 (181)
-+.+.|+.++||.+.+|.|. +..|+| .+ ..+.|+.|+..-+..+|.+.=++=.+
T Consensus 111 EL~rtI~~i~~V~~ArVhl~~P~~~~f~~~~~~~sASV~l~~~~g~~l~~qv~~I~~LVa~SV~~L~~enVt 182 (193)
T TIGR02544 111 RLEQTLSQIDGVISARVHVVLPENDNNGRPKKPSSASVFIKYRPGLNLDALIPKIKRLVANSIPGLDYDNVS 182 (193)
T ss_pred HHHHHHHhcCCeeeeEEEEECCCCCcccccCCCCcEEEEEEeCCCCCcHHHHHHHHHHHHHhcCCCCccceE
Confidence 36678889999999999882 345555 11 22337777777777777766554433
No 36
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=39.65 E-value=52 Score=26.53 Aligned_cols=51 Identities=12% Similarity=0.167 Sum_probs=30.9
Q ss_pred cCCCceeeEEEEecceEEE----eeeccccccchHHHHHHHHHhCCccceeeccccc
Q 030235 122 GTEGISDLKVQVIEGIATV----EKQTTVQATGVAANLVEIIQGSGFKLQTLNLSFD 174 (181)
Q Consensus 122 ~leGVsdVkVsLeeG~AtV----~kqttvqatgvassLvEAIe~aGFevqtl~lsf~ 174 (181)
.+.-|.+|+| +++.+.| +-..-.....+...|+++++..|++-..+++.++
T Consensus 13 dLG~Vr~V~v--~gd~V~VtIt~Ty~gcpa~e~L~~~I~~aL~~~Gv~~V~V~i~~~ 67 (146)
T TIGR02159 13 DLGMVREVDV--DGGGVVVKFTPTYSGCPALEVIRQDIRDAVRALGVEVVEVSTSLD 67 (146)
T ss_pred hcCCeeEEEE--ECCEEEEEEEeCCCCCchHHHHHHHHHHHHHhcCCCeEEEeEeeC
Confidence 4444565444 5666666 2222333334567788888888887777776664
No 37
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=39.31 E-value=55 Score=24.67 Aligned_cols=38 Identities=21% Similarity=0.344 Sum_probs=30.4
Q ss_pred cCCcceEEEEeeccCCCCCchHHHHHHhccCCCceeeEEE
Q 030235 93 SPSDKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQ 132 (181)
Q Consensus 93 ~~sd~l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVs 132 (181)
+---.|.+++--+-. ++-...+..++++++||+.|+|.
T Consensus 46 FGLkaL~i~~vv~D~--~~~td~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 46 FGLKALKLYVIMPDE--EGGTEPVEEAFANVEGVESVEVE 83 (88)
T ss_pred ccceeEEEEEEEEcC--CcCcHHHHHHHhccCCCcEEEEE
Confidence 556678888765444 56779999999999999999985
No 38
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=38.64 E-value=1.2e+02 Score=21.86 Aligned_cols=30 Identities=20% Similarity=0.335 Sum_probs=22.3
Q ss_pred CCchHHHHHHhccCCCceeeEEEEecceEEE
Q 030235 110 ETAIPAVTQALQGTEGISDLKVQVIEGIATV 140 (181)
Q Consensus 110 e~cV~sVTkALE~leGVsdVkVsLeeG~AtV 140 (181)
..-...|.++|.++||| +|.-.-++|+..|
T Consensus 14 p~~~~~v~~~l~~~~gv-EVh~~~~~GKiVV 43 (79)
T PF03927_consen 14 PERLEEVAEALAAIPGV-EVHAVDEDGKIVV 43 (79)
T ss_dssp CCCHHHHHHHHCCSTTE-EEEEEETTTEEEE
T ss_pred chhHHHHHHHHHcCCCc-EEEeeCCCCeEEE
Confidence 35678999999999998 5554445477666
No 39
>PF06345 Drf_DAD: DRF Autoregulatory Domain; InterPro: IPR010465 This domain is found in Diaphanous-related formins (Drfs). It binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of diaphanous activating domains (DAD) to mammalian cells induces actin filament formation, stabilises microtubules, and activates serum-response mediated transcription [].; PDB: 3O4X_H 3OBV_E 2BAP_C 2F31_B.
Probab=36.74 E-value=28 Score=19.27 Aligned_cols=12 Identities=42% Similarity=0.637 Sum_probs=9.7
Q ss_pred chHHHHHHHHHh
Q 030235 150 GVAANLVEIIQG 161 (181)
Q Consensus 150 gvassLvEAIe~ 161 (181)
||+++|.||++.
T Consensus 1 gvmdsllealqt 12 (15)
T PF06345_consen 1 GVMDSLLEALQT 12 (15)
T ss_dssp -HHHHHHHHHHH
T ss_pred CcHHHHHHHHHc
Confidence 789999999874
No 40
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=36.59 E-value=26 Score=26.18 Aligned_cols=18 Identities=22% Similarity=0.547 Sum_probs=16.5
Q ss_pred HHHHHHHHhCCccceeec
Q 030235 153 ANLVEIIQGSGFKLQTLN 170 (181)
Q Consensus 153 ssLvEAIe~aGFevqtl~ 170 (181)
+.++++++..||++..|.
T Consensus 11 s~v~~~L~~~GyeVv~l~ 28 (80)
T PF03698_consen 11 SNVKEALREKGYEVVDLE 28 (80)
T ss_pred hHHHHHHHHCCCEEEecC
Confidence 578999999999999987
No 41
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=35.46 E-value=1.1e+02 Score=18.94 Aligned_cols=59 Identities=8% Similarity=0.207 Sum_probs=33.7
Q ss_pred CCCchHHHHHHhccCCC-ceeeEEEEe-----cceEEEeeeccccccchHHHHHHHHHhCCccce
Q 030235 109 NETAIPAVTQALQGTEG-ISDLKVQVI-----EGIATVEKQTTVQATGVAANLVEIIQGSGFKLQ 167 (181)
Q Consensus 109 ~e~cV~sVTkALE~leG-VsdVkVsLe-----eG~AtV~kqttvqatgvassLvEAIe~aGFevq 167 (181)
..|.+..|.++|....+ |.++...-. .+.+.+.=.+.+....=...|.+.|+..||++.
T Consensus 8 ~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~~~~l~~l~~~l~~~g~~~~ 72 (73)
T cd04886 8 RPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRGAEHIEEIIAALREAGYDVR 72 (73)
T ss_pred CCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeCCHHHHHHHHHHHHHcCCEEe
Confidence 35678899999987632 233333322 345444111111111124699999999999874
No 42
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=35.36 E-value=1.2e+02 Score=19.51 Aligned_cols=52 Identities=10% Similarity=0.219 Sum_probs=32.5
Q ss_pred CCchHHHHHHhccCCCc--eeeEEEEe--cceEEE---eeeccccccchHHHHHHHHHhCCcccee
Q 030235 110 ETAIPAVTQALQGTEGI--SDLKVQVI--EGIATV---EKQTTVQATGVAANLVEIIQGSGFKLQT 168 (181)
Q Consensus 110 e~cV~sVTkALE~leGV--sdVkVsLe--eG~AtV---~kqttvqatgvassLvEAIe~aGFevqt 168 (181)
.|.+.+|.+.|.+- |+ .++...-. .+.+.+ ....+ .+.++++|+.+||++.-
T Consensus 12 pG~l~~i~~~l~~~-~inI~~i~~~~~~~~~~~~v~i~v~~~~------~~~~~~~L~~~G~~v~~ 70 (72)
T cd04883 12 PGQLADIAAIFKDR-GVNIVSVLVYPSKEEDNKILVFRVQTMN------PRPIIEDLRRAGYEVLW 70 (72)
T ss_pred CCHHHHHHHHHHHc-CCCEEEEEEeccCCCCeEEEEEEEecCC------HHHHHHHHHHCCCeeeC
Confidence 35788899988776 33 33332222 234434 22233 36999999999999853
No 43
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=33.40 E-value=36 Score=26.23 Aligned_cols=23 Identities=30% Similarity=0.536 Sum_probs=19.7
Q ss_pred CCchHHHHHHhccCCCceeeEEE
Q 030235 110 ETAIPAVTQALQGTEGISDLKVQ 132 (181)
Q Consensus 110 e~cV~sVTkALE~leGVsdVkVs 132 (181)
+|-...+.++|++++||.+++|.
T Consensus 61 Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 61 EGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred ccCcHHHHHHHhhccCcceEEEE
Confidence 34578999999999999999874
No 44
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=33.30 E-value=1.1e+02 Score=19.05 Aligned_cols=32 Identities=16% Similarity=0.423 Sum_probs=23.8
Q ss_pred ceEEEEeeccCCCCCchHHHHHHhccCCCceeeEE
Q 030235 97 KLTMYFQADGAMNETAIPAVTQALQGTEGISDLKV 131 (181)
Q Consensus 97 ~l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkV 131 (181)
.-.|+|.-++. .-...+.+.|++++||..+++
T Consensus 40 ~~~~~i~~~~~---~~~~~~~~~L~~~~~v~~v~~ 71 (72)
T cd04874 40 KARIYMELEGV---GDIEELVEELRSLPIVREVEI 71 (72)
T ss_pred eEEEEEEEecc---ccHHHHHHHHhCCCCeEEEEe
Confidence 33456666665 456688899999999998876
No 45
>PRK15124 2'-5' RNA ligase; Provisional
Probab=32.57 E-value=1.4e+02 Score=23.63 Aligned_cols=71 Identities=13% Similarity=0.049 Sum_probs=49.2
Q ss_pred cceEEEEeeccCCCCCchHHHHHHhccCCCceeeEEEEecc------eEEE--eeeccccccchHHHHHHHHHhCCccce
Q 030235 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEG------IATV--EKQTTVQATGVAANLVEIIQGSGFKLQ 167 (181)
Q Consensus 96 d~l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG------~AtV--~kqttvqatgvassLvEAIe~aGFevq 167 (181)
|.|-+-++==|.+++..+..+.++|+.+ ...-.++.++.- .+-| .++.....+-....|.+++..+||...
T Consensus 40 ~nlHiTL~FlG~v~~~~~~~l~~~l~~~-~~~pF~l~l~~~g~Fp~prvlwlg~~~~~~~L~~L~~~l~~~l~~~G~~~e 118 (176)
T PRK15124 40 ANLHLTLAFLGEVSAEKQQALSQLAGRI-RQPGFTLTLDDAGQWPRSRVVWLGMRQPPRGLLQLANMLRSQAARSGCYQS 118 (176)
T ss_pred cccEEEEEecCCCCHHHHHHHHHHHHhc-ccCCeEEEECcccCcCCCCEEEEEcCCCCHHHHHHHHHHHHHHHHcCCCCC
Confidence 4555555556779999999999999988 446677777652 2223 223344566678888889999999654
No 46
>PF13399 LytR_C: LytR cell envelope-related transcriptional attenuator
Probab=31.63 E-value=41 Score=23.49 Aligned_cols=20 Identities=25% Similarity=0.620 Sum_probs=18.1
Q ss_pred cchHHHHHHHHHhCCcccee
Q 030235 149 TGVAANLVEIIQGSGFKLQT 168 (181)
Q Consensus 149 tgvassLvEAIe~aGFevqt 168 (181)
.|.|+.+.+.+++.||.+..
T Consensus 15 ~GlA~~~a~~L~~~Gf~v~~ 34 (90)
T PF13399_consen 15 SGLAARVADALRNRGFTVVE 34 (90)
T ss_pred cCHHHHHHHHHHHCCCceee
Confidence 58999999999999999964
No 47
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=30.28 E-value=43 Score=28.37 Aligned_cols=28 Identities=21% Similarity=0.323 Sum_probs=22.5
Q ss_pred hHHHHHHhccCCCceeeEE--EEecceEEE
Q 030235 113 IPAVTQALQGTEGISDLKV--QVIEGIATV 140 (181)
Q Consensus 113 V~sVTkALE~leGVsdVkV--sLeeG~AtV 140 (181)
=..++++|+.|+||.+|+| +|+.+.-.+
T Consensus 63 E~~L~~iL~~I~GvG~V~VmItl~s~~e~v 92 (186)
T TIGR02830 63 ENELKEILEKIEGVGDVTVMVNLDSSEEKV 92 (186)
T ss_pred HHHHHHHHHhccCcceeEEEEEECCCceEE
Confidence 3678999999999999886 566666666
No 48
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ 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 that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=30.07 E-value=1.5e+02 Score=24.34 Aligned_cols=29 Identities=17% Similarity=0.252 Sum_probs=26.6
Q ss_pred chHHHHHHhccCCCceeeEEEEecceEEE
Q 030235 112 AIPAVTQALQGTEGISDLKVQVIEGIATV 140 (181)
Q Consensus 112 cV~sVTkALE~leGVsdVkVsLeeG~AtV 140 (181)
--..+++....++||.++.|-+-+..|-|
T Consensus 55 ~A~~Ia~~v~~v~~V~dA~vvVtg~~A~V 83 (158)
T TIGR02898 55 VADEIASEAAKVKGVKDATVVITGNYAYV 83 (158)
T ss_pred HHHHHHHHHhcCCCCceEEEEEECCEEEE
Confidence 45678999999999999999999999999
No 49
>PRK03094 hypothetical protein; Provisional
Probab=28.71 E-value=43 Score=25.23 Aligned_cols=19 Identities=11% Similarity=0.401 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCccceeecc
Q 030235 153 ANLVEIIQGSGFKLQTLNL 171 (181)
Q Consensus 153 ssLvEAIe~aGFevqtl~l 171 (181)
+.|+++++..||+|..|+-
T Consensus 11 s~i~~~L~~~GYeVv~l~~ 29 (80)
T PRK03094 11 TDVQQALKQKGYEVVQLRS 29 (80)
T ss_pred HHHHHHHHHCCCEEEecCc
Confidence 5689999999999999974
No 50
>PLN02633 palmitoyl protein thioesterase family protein
Probab=28.30 E-value=1.3e+02 Score=27.67 Aligned_cols=80 Identities=18% Similarity=0.118 Sum_probs=56.3
Q ss_pred eeecCCcceEEEEeeccCCCCCchHHHHHHhccCCCceeeEEEEecc-eEEEeeeccccccchHHHHHH-HHHhCCccce
Q 030235 90 VPVSPSDKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEG-IATVEKQTTVQATGVAANLVE-IIQGSGFKLQ 167 (181)
Q Consensus 90 ~p~~~sd~l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG-~AtV~kqttvqatgvassLvE-AIe~aGFevq 167 (181)
+|++-+--++++-----+-...-+.+|++.|+.++|+--.-|.+.++ .+++-.+.+-|+-+|.+.|++ ....-||.+-
T Consensus 20 ~~~~~~~P~ViwHG~GD~c~~~g~~~~~~l~~~~~g~~~~~i~ig~~~~~s~~~~~~~Qve~vce~l~~~~~l~~G~naI 99 (314)
T PLN02633 20 VHVSVSVPFIMLHGIGTQCSDATNANFTQLLTNLSGSPGFCLEIGNGVGDSWLMPLTQQAEIACEKVKQMKELSQGYNIV 99 (314)
T ss_pred ccccCCCCeEEecCCCcccCCchHHHHHHHHHhCCCCceEEEEECCCccccceeCHHHHHHHHHHHHhhchhhhCcEEEE
Confidence 55665556666654434444457889999999999998888888775 234477788888899999987 3334477664
Q ss_pred ee
Q 030235 168 TL 169 (181)
Q Consensus 168 tl 169 (181)
..
T Consensus 100 Gf 101 (314)
T PLN02633 100 GR 101 (314)
T ss_pred EE
Confidence 44
No 51
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=27.80 E-value=63 Score=24.35 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=27.6
Q ss_pred cCCcceEEEEeeccCCCCCchHHHHHHhccCCCceeeEEE
Q 030235 93 SPSDKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQ 132 (181)
Q Consensus 93 ~~sd~l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVs 132 (181)
.---.|.+++--+-. ++-...+..++++++||+.++|.
T Consensus 46 FGLkaL~~~~vv~D~--~g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 46 FGLVAINVMVVMGDA--EGGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred ccceeeEEEEEEecC--CcChHHHHHHHhcCCCccEEEEE
Confidence 344566777654322 25568999999999999999985
No 52
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=25.30 E-value=1.8e+02 Score=29.77 Aligned_cols=49 Identities=8% Similarity=0.210 Sum_probs=31.4
Q ss_pred HHHHHHhccCCCceeeEEEEecceEEE-eeeccccccch-HHHHHHHHHhC
Q 030235 114 PAVTQALQGTEGISDLKVQVIEGIATV-EKQTTVQATGV-AANLVEIIQGS 162 (181)
Q Consensus 114 ~sVTkALE~leGVsdVkVsLeeG~AtV-~kqttvqatgv-assLvEAIe~a 162 (181)
..++..|+.++||++|++.-.+.+..| -.+.-.++-|+ .+.+..+|+..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 160 SNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 558899999999999998765545555 32222223333 26666777653
No 53
>COG1606 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]
Probab=25.26 E-value=1e+02 Score=27.98 Aligned_cols=54 Identities=17% Similarity=0.328 Sum_probs=39.4
Q ss_pred HHhccCCCceeeEEEEecceEEE-eeeccc-cccchHHHHHHHHHhCCccceeeccc
Q 030235 118 QALQGTEGISDLKVQVIEGIATV-EKQTTV-QATGVAANLVEIIQGSGFKLQTLNLS 172 (181)
Q Consensus 118 kALE~leGVsdVkVsLeeG~AtV-~kqttv-qatgvassLvEAIe~aGFevqtl~ls 172 (181)
..|-.+ |+.++.|.-..+.|.+ ..+-.+ +.-+=...|.+.++..||..++|+|.
T Consensus 198 ~~l~~l-~~~~irvr~~~~~A~iEv~~ee~~k~~~~~~~i~~~lk~~Gf~~VtldLe 253 (269)
T COG1606 198 EFLREL-GVRQIRVRSEDNLAVIEVGPEEPEKLLNEVEEIDDKLKKVGFRKVTLDLE 253 (269)
T ss_pred HHHHHh-hhceeeeeecCceeEEecCccCHHHHhhhHHHHHHHHHHhccceEEechh
Confidence 345667 5999999999999999 332111 22233456899999999999999984
No 54
>PRK12378 hypothetical protein; Provisional
Probab=25.17 E-value=71 Score=27.74 Aligned_cols=70 Identities=14% Similarity=0.232 Sum_probs=41.2
Q ss_pred ceEEEEeeccCCCCC--chHHH-HHHhccCCCceeeEEEEecceEEE-eeeccccccchHHHHHHHHHhCCccceeeccc
Q 030235 97 KLTMYFQADGAMNET--AIPAV-TQALQGTEGISDLKVQVIEGIATV-EKQTTVQATGVAANLVEIIQGSGFKLQTLNLS 172 (181)
Q Consensus 97 ~l~m~f~aegt~~e~--cV~sV-TkALE~leGVsdVkVsLeeG~AtV-~kqttvqatgvassLvEAIe~aGFevqtl~ls 172 (181)
+...+|.--|-+.=. -...+ .-||++ |+.+-+|.-+++.-.| +.+.+. ..++++++..||++..-.|.
T Consensus 126 sv~~~Fe~kG~i~i~~~~~d~~~e~aiea--Ga~~edv~~~~~~~~i~t~p~~~------~~v~~~L~~~g~~~~~sei~ 197 (235)
T PRK12378 126 SVAFMFDHKGVFVFEGDDEDELLEALIDA--DVDVEDVEEEEGTITVYTDPTDF------HKVKKALEAAGIEFLVAELE 197 (235)
T ss_pred ceeeeeecceEEEeCCCCHHHHHHHHHhC--CCCcccccccCCeEEEEECHHHH------HHHHHHHHHcCCCceeeEEE
Confidence 345566655543211 11222 234553 5522233345666666 778885 89999999999998777666
Q ss_pred cc
Q 030235 173 FD 174 (181)
Q Consensus 173 f~ 174 (181)
|-
T Consensus 198 ~~ 199 (235)
T PRK12378 198 MI 199 (235)
T ss_pred Ee
Confidence 64
No 55
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=24.52 E-value=69 Score=27.68 Aligned_cols=53 Identities=25% Similarity=0.377 Sum_probs=36.4
Q ss_pred hHHHHHHhccCCCceeeEEEEecceEEE-ee--eccccccchHHHHHHHHHhCCccce
Q 030235 113 IPAVTQALQGTEGISDLKVQVIEGIATV-EK--QTTVQATGVAANLVEIIQGSGFKLQ 167 (181)
Q Consensus 113 V~sVTkALE~leGVsdVkVsLeeG~AtV-~k--qttvqatgvassLvEAIe~aGFevq 167 (181)
-..|+++|++.-|| ++.+++.+|.+++ +. ..|+-+.==|..+++|| +.||..+
T Consensus 26 ~g~v~k~ie~~~~~-~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAI-grGF~pe 81 (194)
T COG1094 26 WGEVKKAIEEKTGV-KLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAI-GRGFPPE 81 (194)
T ss_pred cccchHHHHhhcCe-EEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHH-hcCCCHH
Confidence 34688999999775 6889999999999 33 34553334455666666 4677654
No 56
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=24.50 E-value=1.4e+02 Score=30.42 Aligned_cols=53 Identities=13% Similarity=0.312 Sum_probs=39.3
Q ss_pred CCCCchHHHHHHhccCCCceeeEEEEecceEEE----eeeccccccchHHHHHHHHHhC
Q 030235 108 MNETAIPAVTQALQGTEGISDLKVQVIEGIATV----EKQTTVQATGVAANLVEIIQGS 162 (181)
Q Consensus 108 ~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV----~kqttvqatgvassLvEAIe~a 162 (181)
+++.-.+.++++|.+++||++++-.-.+|.+.+ ...+++ .-..+.+++.|.++
T Consensus 59 ve~~vt~piE~~l~~i~gv~~i~S~s~~G~s~i~l~f~~~~d~--~~a~~~v~~~v~~~ 115 (1025)
T PRK10614 59 MASSVATPLERSLGRIAGVNEMTSSSSLGSTRIILQFDFDRDI--NGAARDVQAAINAA 115 (1025)
T ss_pred HHHHHHHHHHHHhcCCCCceEEEEEecCCeEEEEEEEECCCCh--HHHHHHHHHHHHHH
Confidence 344556889999999999999999999999999 334443 22356677777653
No 57
>PF05430 Methyltransf_30: S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR008471 This entry contains several uncharacterised bacterial proteins with no known function.; GO: 0016645 oxidoreductase activity, acting on the CH-NH group of donors, 0055114 oxidation-reduction process; PDB: 2E58_D 3SGL_A 3PVC_A 3AWI_D 3PS9_A 2QY6_A.
Probab=24.49 E-value=47 Score=25.86 Aligned_cols=18 Identities=22% Similarity=0.516 Sum_probs=15.9
Q ss_pred HHHHHHHHHhCCccceee
Q 030235 152 AANLVEIIQGSGFKLQTL 169 (181)
Q Consensus 152 assLvEAIe~aGFevqtl 169 (181)
|..++++++.+||+++..
T Consensus 92 a~~Vr~~L~~aGF~v~~~ 109 (124)
T PF05430_consen 92 AGAVRRALQQAGFEVEKV 109 (124)
T ss_dssp BHHHHHHHHHCTEEEEEE
T ss_pred hHHHHHHHHHcCCEEEEc
Confidence 588999999999999754
No 58
>PRK11026 ftsX cell division ABC transporter subunit FtsX; Provisional
Probab=23.86 E-value=69 Score=28.19 Aligned_cols=32 Identities=25% Similarity=0.569 Sum_probs=26.5
Q ss_pred eEEEEeeccCCCCCchHHHHHHhccCCCceeeEE
Q 030235 98 LTMYFQADGAMNETAIPAVTQALQGTEGISDLKV 131 (181)
Q Consensus 98 l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkV 131 (181)
.+.|+|.+ +.+.-+.++.+.|++++||++|+.
T Consensus 68 i~vyl~~~--~~~~~~~~l~~~L~~~~~V~~v~~ 99 (309)
T PRK11026 68 LTVYLDKT--LDDDAANAVVEQLKAEDGVEKVNY 99 (309)
T ss_pred EEEEECCC--CCHHHHHHHHHHHhCCCCcceEEE
Confidence 56677643 777889999999999999999876
No 59
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=23.51 E-value=90 Score=21.11 Aligned_cols=47 Identities=21% Similarity=0.310 Sum_probs=31.9
Q ss_pred eeEEEEecceEE-E--eeeccccccchHHHHHHHHHh-CCccceeecccccCccccc
Q 030235 128 DLKVQVIEGIAT-V--EKQTTVQATGVAANLVEIIQG-SGFKLQTLNLSFDDEEEVL 180 (181)
Q Consensus 128 dVkVsLeeG~At-V--~kqttvqatgvassLvEAIe~-aGFevqtl~lsf~d~~~~~ 180 (181)
.+|+...++.-+ + +...+- +.|++.|+. .|..-..+.|.+.|+|..+
T Consensus 3 ~vK~~~~~~~~~~~~~~~~~s~------~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~ 53 (84)
T PF00564_consen 3 RVKVRYGGDIRRIISLPSDVSF------DDLRSKIREKFGLLDEDFQLKYKDEDGDL 53 (84)
T ss_dssp EEEEEETTEEEEEEEECSTSHH------HHHHHHHHHHHTTSTSSEEEEEEETTSSE
T ss_pred EEEEEECCeeEEEEEcCCCCCH------HHHHHHHHHHhCCCCccEEEEeeCCCCCE
Confidence 467777777777 5 555563 667776665 5555688889998877643
No 60
>PRK15368 pathogenicity island chaperone protein SpiC; Provisional
Probab=23.12 E-value=88 Score=25.70 Aligned_cols=50 Identities=12% Similarity=0.180 Sum_probs=43.9
Q ss_pred eecCCcceEEEEeeccCCCCCchHHHHHHhccCCCceeeEEEEecceEEE
Q 030235 91 PVSPSDKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATV 140 (181)
Q Consensus 91 p~~~sd~l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV 140 (181)
--.-|=-+.+||-.--.+++.||.-||=-|-+.||+-|--++|..|--=+
T Consensus 36 ~~~hS~~i~if~~e~k~isd~~i~YITLmLaA~~d~hDyAlQL~~~~~WL 85 (127)
T PRK15368 36 IFSEAFSISLFLNDLESLPKPCLAYVTLLLAAHPDVHDYAIQLTADGGWL 85 (127)
T ss_pred eeeccEEEEEEEeehhcCcHHHHHHHHHHHHhCCCchhheeEeccCcEEE
Confidence 34556678899999999999999999999999999999999999886655
No 61
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.54 E-value=68 Score=20.10 Aligned_cols=52 Identities=21% Similarity=0.202 Sum_probs=29.7
Q ss_pred CCchHHHHHHhccCCC-ceeeEEEEec--ceEEEeeeccccccchHHHHHHHHHhCCccc
Q 030235 110 ETAIPAVTQALQGTEG-ISDLKVQVIE--GIATVEKQTTVQATGVAANLVEIIQGSGFKL 166 (181)
Q Consensus 110 e~cV~sVTkALE~leG-VsdVkVsLee--G~AtV~kqttvqatgvassLvEAIe~aGFev 166 (181)
.|-+.++.+.|.+-.. |.++...-.. |.+.+.=.++- .+.+.+.++.+||++
T Consensus 10 pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve~-----~~~~~~~L~~~G~~v 64 (65)
T cd04882 10 PGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTED-----IEKAIEVLQERGVEL 64 (65)
T ss_pred CcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeCC-----HHHHHHHHHHCCceE
Confidence 4566777777766631 2333332222 34444111111 479999999999975
No 62
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=22.52 E-value=80 Score=26.33 Aligned_cols=52 Identities=15% Similarity=0.282 Sum_probs=33.0
Q ss_pred HHHHHhccCCCceeeEEEEec------------ceEEE---ee---eccccccchHHHHHHHHHhCCccc
Q 030235 115 AVTQALQGTEGISDLKVQVIE------------GIATV---EK---QTTVQATGVAANLVEIIQGSGFKL 166 (181)
Q Consensus 115 sVTkALE~leGVsdVkVsLee------------G~AtV---~k---qttvqatgvassLvEAIe~aGFev 166 (181)
.+.+.|+.++||.+.+|.|.- ..|+| .+ ..+.|+.|+..-+.-+|.+.-.+=
T Consensus 119 eL~~tI~~i~gV~~A~V~l~~Pe~~~f~~~~~~~sASV~l~~~~g~~l~~qv~~I~~LVa~sV~gL~~en 188 (206)
T PF01514_consen 119 ELERTIESIDGVESARVHLVLPERSVFGENQQPPSASVVLKLKPGSELSEQVQGIQNLVASSVPGLKPEN 188 (206)
T ss_dssp HHHHHHTTSTTEEEEEEEEEE----BTTB----EEEEEEEEE-TTS--GGGHHHHHHHHHHHSTT--GGG
T ss_pred HHHHHHHcCCCeeEEEEEEecCCccccccCCCCCeEEEEEEECCCCChHHHHHHHHHHHHHhcCCCCccc
Confidence 366788999999999999742 34555 11 222567777777777776665544
No 63
>PRK13558 bacterio-opsin activator; Provisional
Probab=22.28 E-value=4.3e+02 Score=24.44 Aligned_cols=63 Identities=19% Similarity=0.291 Sum_probs=44.8
Q ss_pred cceEEEEeeccCCCCCchHHHHHHhccCCCceeeEEE-EecceEEEeeeccccccchHHHHHHHHHhCCcccee
Q 030235 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQ-VIEGIATVEKQTTVQATGVAANLVEIIQGSGFKLQT 168 (181)
Q Consensus 96 d~l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkVs-LeeG~AtV~kqttvqatgvassLvEAIe~aGFevqt 168 (181)
+...+||-.+|. -...|..+|++.++|.++++- -.++.+.+.-..+- ..+..++.+.|.-+..
T Consensus 485 ~~~~~~~~~~~~----~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~g~~~~~ 548 (665)
T PRK13558 485 GGVLVLFTVPGD----DATALVDAAADYDAVQDVRVLVSTDDECLVEFTLSG------DSLVRLLSERGGRVQD 548 (665)
T ss_pred CCEEEEEEEeCC----CHHHHHHhhhccCCcceEEEEEecCCceEEEEEecC------CcHhHhhHhcCCEEEE
Confidence 458899988864 257899999999999999884 45555555222221 4677888888877765
No 64
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=22.26 E-value=1.6e+02 Score=19.09 Aligned_cols=29 Identities=24% Similarity=0.377 Sum_probs=15.8
Q ss_pred HHHHHhcc---CCCceeeEEEEecceEEEeeec
Q 030235 115 AVTQALQG---TEGISDLKVQVIEGIATVEKQT 144 (181)
Q Consensus 115 sVTkALE~---leGVsdVkVsLeeG~AtV~kqt 144 (181)
+|.++|.. +++- +++|...+|.+.+...+
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v 34 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGEV 34 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEEE
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEeeC
Confidence 45566665 5555 78999999999994444
No 65
>TIGR00325 lpxC UDP-3-0-acyl N-acetylglucosamine deacetylase. UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase from E. coli, LpxC, was previously designated EnvA. This enzyme is involved in lipid-A precursor biosynthesis. It is essential for cell viability.
Probab=21.79 E-value=1.7e+02 Score=26.64 Aligned_cols=50 Identities=18% Similarity=0.341 Sum_probs=39.1
Q ss_pred CchHHHHHHhccCCCceeeEEEEecceEEEeeeccccccchHHHHHHHHHhCCcccee
Q 030235 111 TAIPAVTQALQGTEGISDLKVQVIEGIATVEKQTTVQATGVAANLVEIIQGSGFKLQT 168 (181)
Q Consensus 111 ~cV~sVTkALE~leGVsdVkVsLeeG~AtV~kqttvqatgvassLvEAIe~aGFevqt 168 (181)
.-|-.+=.||.++ ||.|+.|.++..+.=+ .-|=|..-+++|+++|.+-|.
T Consensus 73 ~TVEHLmAAL~gl-gIDN~~Ieidg~EvPI-------lDGSa~~fv~~i~~aGi~~q~ 122 (297)
T TIGR00325 73 STVEHLLAALAAL-GIDNLRIEVNAPEIPI-------MDGSALPFLYLLLDAGIRELN 122 (297)
T ss_pred EeHHHHHHHHHhC-CCceEEEEeCCCCCCc-------cCCchHHHHHHHHhcCCeecC
Confidence 4577778889999 9999999998875544 334467889999999987554
No 66
>TIGR00439 ftsX putative protein insertion permease FtsX. FtsX is an integral membrane protein encoded in the same operon as signal recognition particle docking protein FtsY and FtsE. It belongs to a family of predicted permeases and may play a role in the insertion of proteins required for potassium transport, cell division, and other activities. FtsE is a hydrophilic nucleotide-binding protein that associates with the inner membrane by means of association with FtsX.
Probab=21.54 E-value=82 Score=27.72 Aligned_cols=32 Identities=19% Similarity=0.481 Sum_probs=25.8
Q ss_pred eEEEEeeccCCCCCchHHHHHHhccCCCceeeEE
Q 030235 98 LTMYFQADGAMNETAIPAVTQALQGTEGISDLKV 131 (181)
Q Consensus 98 l~m~f~aegt~~e~cV~sVTkALE~leGVsdVkV 131 (181)
.+.|++. .+++.-+.++.+.|++.|||++|+.
T Consensus 68 i~vyl~~--~~~~~~~~~l~~~l~~~~~V~~v~~ 99 (309)
T TIGR00439 68 ITVYLEK--ALAQSDADTVVSLLTRDKGVENINY 99 (309)
T ss_pred EEEEeCC--CCCHHHHHHHHHHHhCCCCccEEEE
Confidence 4566763 3677778999999999999999886
No 67
>TIGR01033 DNA-binding regulatory protein, YebC/PmpR family. This model describes a minimally characterized protein family, restricted to bacteria excepting for some eukaryotic sequences that have possible transit peptides. YebC from E. coli is crystallized, and PA0964 from Pseudomonas aeruginosa has been shown to be a sequence-specific DNA-binding regulatory protein.
Probab=21.22 E-value=1.3e+02 Score=26.04 Aligned_cols=68 Identities=15% Similarity=0.358 Sum_probs=42.6
Q ss_pred ceEEEEeeccCCCCCc----hHH-HHHHhccCCCceeeEEEEecceEEE-eeeccccccchHHHHHHHHHhCCccceeec
Q 030235 97 KLTMYFQADGAMNETA----IPA-VTQALQGTEGISDLKVQVIEGIATV-EKQTTVQATGVAANLVEIIQGSGFKLQTLN 170 (181)
Q Consensus 97 ~l~m~f~aegt~~e~c----V~s-VTkALE~leGVsdVkVsLeeG~AtV-~kqttvqatgvassLvEAIe~aGFevqtl~ 170 (181)
+...+|.--|.+.=.. ... ..-||+ .|+.||+.+ ++...| ..+.+. ..++++++..||++..-.
T Consensus 129 sv~~~Fe~kG~i~~~~~~~~~d~~~e~aie--aGAedv~~~--~~~~~v~~~~~~~------~~v~~~L~~~g~~i~~se 198 (238)
T TIGR01033 129 SVSYLFSRKGVIEVPKNEVDEEDLMEAAIE--AGAEDIDVD--DDEFEVYTAPEEL------EKVKEALEAKGFPIESAE 198 (238)
T ss_pred ceeeeeecceEEEECCCCCCHHHHHHHHHh--CCCceeecc--CCcEEEEECHHHH------HHHHHHHHHcCCCceeeE
Confidence 3455666655543211 122 233455 388887643 334555 777774 899999999999988777
Q ss_pred cccc
Q 030235 171 LSFD 174 (181)
Q Consensus 171 lsf~ 174 (181)
+.|-
T Consensus 199 i~~~ 202 (238)
T TIGR01033 199 ITMI 202 (238)
T ss_pred EEEe
Confidence 6664
No 68
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.53 E-value=2.9e+02 Score=19.32 Aligned_cols=53 Identities=13% Similarity=0.242 Sum_probs=32.1
Q ss_pred CCchHHHHHHhccCCCceeeEEEE---ecceEEE---ee--eccccccchHHHHHHHHHhCCccceee
Q 030235 110 ETAIPAVTQALQGTEGISDLKVQV---IEGIATV---EK--QTTVQATGVAANLVEIIQGSGFKLQTL 169 (181)
Q Consensus 110 e~cV~sVTkALE~leGVsdVkVsL---eeG~AtV---~k--qttvqatgvassLvEAIe~aGFevqtl 169 (181)
.|...++.++|.+ .+|.++.-+- ..+.+.+ .+ +-. .+.++++++++||++..+
T Consensus 12 PG~L~~ll~~l~~-anI~~~~y~~~~~~~~~v~i~ie~~~~~~~------~~~i~~~L~~~G~~~~~~ 72 (85)
T cd04906 12 PGSFKKFCELIGP-RNITEFNYRYADEKDAHIFVGVSVANGAEE------LAELLEDLKSAGYEVVDL 72 (85)
T ss_pred CcHHHHHHHHhCC-CceeEEEEEccCCCeeEEEEEEEeCCcHHH------HHHHHHHHHHCCCCeEEC
Confidence 3556677777773 3566555544 2333333 21 222 378999999999988653
No 69
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.41 E-value=2.2e+02 Score=17.47 Aligned_cols=29 Identities=14% Similarity=0.195 Sum_probs=22.2
Q ss_pred EEEEeeccCCCCCchHHHHHHhccCCCceeeEE
Q 030235 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKV 131 (181)
Q Consensus 99 ~m~f~aegt~~e~cV~sVTkALE~leGVsdVkV 131 (181)
.++|.-++. -.+.+-+.|++++||.+|..
T Consensus 42 ~i~i~v~~~----~~~~~i~~l~~~~~v~~v~~ 70 (71)
T cd04903 42 LMVIEVDQP----IDEEVIEEIKKIPNIHQVIL 70 (71)
T ss_pred EEEEEeCCC----CCHHHHHHHHcCCCceEEEE
Confidence 455666665 46788999999999999864
No 70
>PRK13187 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed
Probab=20.16 E-value=1.9e+02 Score=26.43 Aligned_cols=63 Identities=17% Similarity=0.227 Sum_probs=43.8
Q ss_pred ceEEEEee-ccCCCCCchHHHHHHhccCCCceeeEEEEecceEEEeeeccccccchHHHHHHHHHhCCcccee
Q 030235 97 KLTMYFQA-DGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVEKQTTVQATGVAANLVEIIQGSGFKLQT 168 (181)
Q Consensus 97 ~l~m~f~a-egt~~e~cV~sVTkALE~leGVsdVkVsLeeG~AtV~kqttvqatgvassLvEAIe~aGFevqt 168 (181)
.|..-... .| ..=.-|-.+=.||.++ ||.|+.|.++..+.=+ .-|=|..-+++|+.+|..-|.
T Consensus 72 ~l~T~L~~~~~-~~V~TVEHLlAAL~gl-gIDN~~Ievdg~EvPI-------lDGSA~~fv~~i~~aGi~~q~ 135 (304)
T PRK13187 72 PLCTMLRNADG-VGVRTVEHLLASLLAC-EIDHAIVELDAEEVPI-------LDGSATPWVDAIRACGRVALD 135 (304)
T ss_pred cceeEEecCCC-cEEeeHHHHHHHHHhC-CCceEEEEeCCCCCCc-------ccCCHHHHHHHHHhcCCeecC
Confidence 34444443 23 3334577777888898 9999999999875433 335567889999999997553
No 71
>PRK10598 lipoprotein; Provisional
Probab=20.12 E-value=52 Score=27.98 Aligned_cols=51 Identities=20% Similarity=0.311 Sum_probs=32.7
Q ss_pred cCCCceeeEEEEecceEEE--eeeccccccchHHHHHHHHHhCCccceeeccccc
Q 030235 122 GTEGISDLKVQVIEGIATV--EKQTTVQATGVAANLVEIIQGSGFKLQTLNLSFD 174 (181)
Q Consensus 122 ~leGVsdVkVsLeeG~AtV--~kqttvqatgvassLvEAIe~aGFevqtl~lsf~ 174 (181)
+++|+.+++++|.+..+++ ..+-.+..+|-+..-+... .|=--.+++|.|+
T Consensus 47 G~~gl~~a~i~l~~l~~~IGr~~~~~v~l~g~a~v~v~~~--~g~~~a~l~l~~~ 99 (186)
T PRK10598 47 GLPGVADAHIVLTNLTSQIGREEPNKVTLTGDANLDISSL--FGSQKADMKLTLK 99 (186)
T ss_pred CCCceeeeEEEeeeceeecCCCCCCEEEEeceeeeeeecc--CCCcCcEEEEEEE
Confidence 7899999999999999999 3434445566555444444 2322244555543
No 72
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=20.07 E-value=2.5e+02 Score=20.93 Aligned_cols=39 Identities=13% Similarity=0.227 Sum_probs=31.4
Q ss_pred cCCcceEEEEeeccCCCCCchHHHHHHh-ccCCCceeeEEEE
Q 030235 93 SPSDKLTMYFQADGAMNETAIPAVTQAL-QGTEGISDLKVQV 133 (181)
Q Consensus 93 ~~sd~l~m~f~aegt~~e~cV~sVTkAL-E~leGVsdVkVsL 133 (181)
+---.|.|++--+- .++-+..+..++ ..++||.+++|.=
T Consensus 46 FGlk~L~v~~vv~D--~~~~~d~lee~i~~~~e~Vqsvei~~ 85 (89)
T PF00736_consen 46 FGLKALQVSCVVED--DEGSTDDLEEAIESFEEGVQSVEIES 85 (89)
T ss_dssp TTEEEEEEEEEECT--TTCGHHHHHHHHTTCTTTEEEEEEEE
T ss_pred ccEEEEEEEEEEEc--CccChHHHHHHHHhcCCCccEEEEEE
Confidence 55667888876655 567899999999 9999999999853
Done!