Query 016666
Match_columns 385
No_of_seqs 181 out of 1091
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 08:54:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016666.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016666hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.3 2.1E-11 4.6E-16 91.6 8.3 58 39-96 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.1 4.7E-10 1E-14 88.5 8.6 66 35-100 1-70 (71)
3 KOG1603 Copper chaperone [Inor 99.1 4.6E-10 9.9E-15 88.7 8.3 68 34-101 3-71 (73)
4 KOG4656 Copper chaperone for s 98.6 1.4E-07 3.1E-12 89.4 8.1 70 36-105 7-76 (247)
5 PLN02957 copper, zinc superoxi 98.1 1.6E-05 3.4E-10 76.0 9.8 71 33-103 3-73 (238)
6 PRK10671 copA copper exporting 97.9 2E-05 4.4E-10 86.7 8.2 64 36-101 3-67 (834)
7 TIGR00003 copper ion binding p 97.8 0.00029 6.4E-09 48.0 8.7 62 36-97 2-67 (68)
8 COG2217 ZntA Cation transport 97.6 0.00014 3.1E-09 79.6 7.7 63 36-99 2-69 (713)
9 PRK10671 copA copper exporting 96.6 0.0058 1.3E-07 67.7 8.2 66 36-101 99-165 (834)
10 PRK11033 zntA zinc/cadmium/mer 96.4 0.012 2.6E-07 64.8 8.7 69 33-101 50-120 (741)
11 KOG0207 Cation transport ATPas 96.4 0.0084 1.8E-07 67.2 7.5 66 36-101 146-215 (951)
12 KOG0207 Cation transport ATPas 96.1 0.013 2.7E-07 65.8 7.2 67 37-103 70-140 (951)
13 TIGR02052 MerP mercuric transp 93.1 1.4 3E-05 33.2 9.6 63 37-99 24-90 (92)
14 cd00371 HMA Heavy-metal-associ 90.1 2.8 6.1E-05 25.3 7.8 55 41-95 3-60 (63)
15 PRK13748 putative mercuric red 82.0 7 0.00015 41.1 8.9 64 39-102 3-69 (561)
16 COG1888 Uncharacterized protei 79.9 9.1 0.0002 32.8 7.1 70 34-103 4-82 (97)
17 PF02680 DUF211: Uncharacteriz 76.4 13 0.00028 31.9 7.1 68 34-102 3-79 (95)
18 PF01883 DUF59: Domain of unkn 59.8 15 0.00032 28.4 3.9 33 36-68 34-72 (72)
19 PRK14054 methionine sulfoxide 50.1 26 0.00057 32.7 4.5 44 47-90 10-75 (172)
20 PRK10553 assembly protein for 48.0 62 0.0013 27.1 6.0 48 44-91 12-61 (87)
21 PF01206 TusA: Sulfurtransfera 39.5 67 0.0015 24.5 4.7 53 39-100 2-57 (70)
22 cd04883 ACT_AcuB C-terminal AC 38.5 1.6E+02 0.0035 21.8 7.5 59 39-97 3-68 (72)
23 PF03927 NapD: NapD protein; 36.7 1.2E+02 0.0027 24.5 6.0 45 48-93 15-60 (79)
24 PF13732 DUF4162: Domain of un 36.4 94 0.002 24.2 5.2 44 57-101 26-70 (84)
25 PRK05528 methionine sulfoxide 36.1 68 0.0015 29.6 4.9 44 47-90 8-68 (156)
26 KOG0260 RNA polymerase II, lar 35.1 2.4E+02 0.0051 34.3 9.8 8 61-68 1256-1263(1605)
27 PRK00058 methionine sulfoxide 34.4 62 0.0013 31.4 4.5 45 46-90 51-117 (213)
28 TIGR03406 FeS_long_SufT probab 34.2 52 0.0011 30.7 3.9 36 37-72 114-155 (174)
29 PF05046 Img2: Mitochondrial l 33.1 2.1E+02 0.0046 23.6 7.0 59 36-95 28-87 (87)
30 PRK13014 methionine sulfoxide 32.6 52 0.0011 31.2 3.6 44 47-90 15-80 (186)
31 cd04888 ACT_PheB-BS C-terminal 31.3 1.3E+02 0.0029 22.5 5.1 34 35-68 40-74 (76)
32 TIGR02945 SUF_assoc FeS assemb 30.7 62 0.0013 26.5 3.4 23 51-73 58-80 (99)
33 cd04908 ACT_Bt0572_1 N-termina 28.5 2.5E+02 0.0054 20.9 7.2 58 40-98 4-65 (66)
34 PRK12757 cell division protein 28.3 2.4E+02 0.0052 28.2 7.5 65 34-100 181-251 (256)
35 KOG4264 Nucleo-cytoplasmic pro 27.2 1.3E+02 0.0029 33.2 5.9 35 291-327 592-627 (694)
36 PF01625 PMSR: Peptide methion 26.8 1.5E+02 0.0033 27.1 5.5 44 47-90 7-72 (155)
37 PRK11670 antiporter inner memb 25.0 2E+02 0.0043 29.5 6.6 66 37-102 48-144 (369)
38 PF09580 Spore_YhcN_YlaJ: Spor 23.5 2E+02 0.0042 25.8 5.6 59 44-102 71-141 (177)
39 KOG4730 D-arabinono-1, 4-lacto 23.1 54 0.0012 35.5 2.1 68 26-98 67-137 (518)
40 cd04909 ACT_PDH-BS C-terminal 23.0 3.2E+02 0.0069 20.2 6.7 59 39-97 3-69 (69)
41 PF04972 BON: BON domain; Int 22.8 57 0.0012 24.2 1.7 31 52-83 3-36 (64)
42 PF13291 ACT_4: ACT domain; PD 22.3 2.3E+02 0.005 21.8 5.1 35 33-67 45-79 (80)
43 PF14437 MafB19-deam: MafB19-l 22.2 1.8E+02 0.0039 26.8 5.0 42 35-77 99-142 (146)
44 PRK05550 bifunctional methioni 21.6 1.3E+02 0.0028 30.4 4.4 46 45-90 132-199 (283)
45 KOG1924 RhoA GTPase effector D 20.6 4.2E+02 0.0092 31.0 8.3 8 274-281 548-555 (1102)
46 PRK07334 threonine dehydratase 20.1 3.7E+02 0.0081 27.6 7.5 64 37-100 326-402 (403)
47 cd04906 ACT_ThrD-I_1 First of 20.0 4.5E+02 0.0098 20.9 8.4 64 39-103 3-75 (85)
No 1
>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=99.27 E-value=2.1e-11 Score=91.62 Aligned_cols=58 Identities=38% Similarity=0.695 Sum_probs=54.2
Q ss_pred EEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEec---CCHHHHHHHHHhcCCc
Q 016666 39 VLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKGD---VAAETLIGKLEKNGKH 96 (385)
Q Consensus 39 ~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG~---id~eeLikaIrKAGy~ 96 (385)
+|+|. |+|.+|+++|+++|++++||.++.+|+.+++|+|.++ ++.++|+++|+++||+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 58998 9999999999999999999999999999999999965 4569999999999994
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.09 E-value=4.7e-10 Score=88.48 Aligned_cols=66 Identities=29% Similarity=0.491 Sum_probs=58.8
Q ss_pred ceEEEEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEE--e-cCCHHHHHHHHHhcCCceeeC
Q 016666 35 CKTWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVK--G-DVAAETLIGKLEKNGKHAELW 100 (385)
Q Consensus 35 ~qTv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVt--G-~id~eeLikaIrKAGy~Aelv 100 (385)
+++..|+|+ |+|.+|+.+|+++|.+++||..++||+..++++|+ + .++.++|+.+|.++||.+..+
T Consensus 1 ~~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 1 MMKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred CceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeeec
Confidence 356789999 99999999999999999999999999999666665 4 489999999999999988754
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.09 E-value=4.6e-10 Score=88.74 Aligned_cols=68 Identities=50% Similarity=0.904 Sum_probs=63.3
Q ss_pred cceEEEEEEeeccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEecCCHHHHHHHHHhcC-CceeeCC
Q 016666 34 KCKTWVLRVSIHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKGDVAAETLIGKLEKNG-KHAELWP 101 (385)
Q Consensus 34 k~qTv~LkVeM~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG~id~eeLikaIrKAG-y~Aelv~ 101 (385)
.+++++++|.|+|.+|..+|++.|+.+.||.++++|...++|+|.|.+++..|++.|++.+ .++.+|.
T Consensus 3 ~~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 3 PIKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred CccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEec
Confidence 4677899999999999999999999999999999999999999999999999999999988 7777764
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.59 E-value=1.4e-07 Score=89.37 Aligned_cols=70 Identities=27% Similarity=0.452 Sum_probs=65.2
Q ss_pred eEEEEEEeeccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEecCCHHHHHHHHHhcCCceeeCCCCch
Q 016666 36 KTWVLRVSIHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKGDVAAETLIGKLEKNGKHAELWPESKA 105 (385)
Q Consensus 36 qTv~LkVeM~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG~id~eeLikaIrKAGy~Aelv~e~~~ 105 (385)
-+++|.|.|+|++|++.|+..|..++||.+|+||+.++.|.|.+.+...+|..+|+.+|.++.++.....
T Consensus 7 ~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~p 76 (247)
T KOG4656|consen 7 YEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGKP 76 (247)
T ss_pred eeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCch
Confidence 3578999999999999999999999999999999999999999999999999999999999998876533
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.11 E-value=1.6e-05 Score=75.97 Aligned_cols=71 Identities=28% Similarity=0.479 Sum_probs=63.8
Q ss_pred ccceEEEEEEeeccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEecCCHHHHHHHHHhcCCceeeCCCC
Q 016666 33 LKCKTWVLRVSIHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKGDVAAETLIGKLEKNGKHAELWPES 103 (385)
Q Consensus 33 ~k~qTv~LkVeM~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG~id~eeLikaIrKAGy~Aelv~e~ 103 (385)
+..+++.|.|.|+|..|+.+|++.|.+++||..+.+|+..++++|...+....|+.+|+++||.++++...
T Consensus 3 ~~~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~ 73 (238)
T PLN02957 3 LPELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQG 73 (238)
T ss_pred CCcEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCC
Confidence 34566778888999999999999999999999999999999999988778899999999999998888764
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.95 E-value=2e-05 Score=86.72 Aligned_cols=64 Identities=23% Similarity=0.418 Sum_probs=57.8
Q ss_pred eEEEEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEecCCHHHHHHHHHhcCCceeeCC
Q 016666 36 KTWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKGDVAAETLIGKLEKNGKHAELWP 101 (385)
Q Consensus 36 qTv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG~id~eeLikaIrKAGy~Aelv~ 101 (385)
++++|+|+ |+|.+|+.+|+++|.+++||..+.||+. +++|+..++.+.|..+|+++||.+++..
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 57899999 9999999999999999999999999994 5666677899999999999999988764
No 7
>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=97.76 E-value=0.00029 Score=47.97 Aligned_cols=62 Identities=18% Similarity=0.410 Sum_probs=52.7
Q ss_pred eEEEEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEe---cCCHHHHHHHHHhcCCce
Q 016666 36 KTWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKG---DVAAETLIGKLEKNGKHA 97 (385)
Q Consensus 36 qTv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG---~id~eeLikaIrKAGy~A 97 (385)
++..|.|. |+|..|...|++.|..+.+|..+.+++...++.|.. ..+...|...+...||.+
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 45678999 999999999999999999999999999999998874 256777777788888753
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.59 E-value=0.00014 Score=79.55 Aligned_cols=63 Identities=25% Similarity=0.514 Sum_probs=56.8
Q ss_pred eEEEEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEec---CC-HHHHHHHHHhcCCceee
Q 016666 36 KTWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKGD---VA-AETLIGKLEKNGKHAEL 99 (385)
Q Consensus 36 qTv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG~---id-~eeLikaIrKAGy~Ael 99 (385)
.+..|.|. |+|..|+++|| +|.+++||..+.||+.+++++|..+ .+ .+++..+++++||.+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 45789999 99999999999 9999999999999999999999743 45 68999999999998765
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.62 E-value=0.0058 Score=67.68 Aligned_cols=66 Identities=26% Similarity=0.497 Sum_probs=58.7
Q ss_pred eEEEEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEecCCHHHHHHHHHhcCCceeeCC
Q 016666 36 KTWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKGDVAAETLIGKLEKNGKHAELWP 101 (385)
Q Consensus 36 qTv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG~id~eeLikaIrKAGy~Aelv~ 101 (385)
.++.|.|. |+|..|...|++.|.+++||..+.+++..+++.|....+.++|...++++||.+.++.
T Consensus 99 ~~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~~ 165 (834)
T PRK10671 99 DSQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAIE 165 (834)
T ss_pred ceEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccccc
Confidence 35778899 9999999999999999999999999999999888766778889899999999876554
No 10
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.38 E-value=0.012 Score=64.78 Aligned_cols=69 Identities=22% Similarity=0.368 Sum_probs=56.8
Q ss_pred ccceEEEEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEec-CCHHHHHHHHHhcCCceeeCC
Q 016666 33 LKCKTWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKGD-VAAETLIGKLEKNGKHAELWP 101 (385)
Q Consensus 33 ~k~qTv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG~-id~eeLikaIrKAGy~Aelv~ 101 (385)
...+++.|.|. |+|..|..+|++.|.+++||..+.+++...++.|... ...+++...++++||.+..+.
T Consensus 50 ~~~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~~~ 120 (741)
T PRK11033 50 VSGTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRDEQ 120 (741)
T ss_pred CCCceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhccccccccc
Confidence 44556788999 9999999999999999999999999999999888632 122677788899999876543
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.37 E-value=0.0084 Score=67.19 Aligned_cols=66 Identities=24% Similarity=0.433 Sum_probs=60.5
Q ss_pred eEEEEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEe---cCCHHHHHHHHHhcCCceeeCC
Q 016666 36 KTWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKG---DVAAETLIGKLEKNGKHAELWP 101 (385)
Q Consensus 36 qTv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG---~id~eeLikaIrKAGy~Aelv~ 101 (385)
+++.|.|. |+|..|..+|++.|.+++||.++.+++.++++.|.. .+.+.+|++.|+..||.+....
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~ 215 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRP 215 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeee
Confidence 67899999 999999999999999999999999999999999974 3788999999999999866555
No 12
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.10 E-value=0.013 Score=65.82 Aligned_cols=67 Identities=24% Similarity=0.373 Sum_probs=61.5
Q ss_pred EEEEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEe---cCCHHHHHHHHHhcCCceeeCCCC
Q 016666 37 TWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKG---DVAAETLIGKLEKNGKHAELWPES 103 (385)
Q Consensus 37 Tv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG---~id~eeLikaIrKAGy~Aelv~e~ 103 (385)
+..|+|. |+|..|.+.|++.|+++.||.++.|.+...+.+|.. .++.+.+.+.++++||.+.++...
T Consensus 70 ~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~ 140 (951)
T KOG0207|consen 70 KCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESV 140 (951)
T ss_pred eeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhcc
Confidence 6789999 999999999999999999999999999999999973 378899999999999999888764
No 13
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=93.13 E-value=1.4 Score=33.23 Aligned_cols=63 Identities=24% Similarity=0.396 Sum_probs=49.0
Q ss_pred EEEEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEe---cCCHHHHHHHHHhcCCceee
Q 016666 37 TWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKG---DVAAETLIGKLEKNGKHAEL 99 (385)
Q Consensus 37 Tv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG---~id~eeLikaIrKAGy~Ael 99 (385)
++.+.+. +.|..|...++..+....+|..+.+++....+.+.. ..+...+...+.+.|+.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 3456778 999999999999999999998888988888766652 24566666667788887554
No 14
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=90.07 E-value=2.8 Score=25.29 Aligned_cols=55 Identities=35% Similarity=0.628 Sum_probs=38.6
Q ss_pred EEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEec--CCHHHHHHHHHhcCC
Q 016666 41 RVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKGD--VAAETLIGKLEKNGK 95 (385)
Q Consensus 41 kVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG~--id~eeLikaIrKAGy 95 (385)
.+. +.|..|...++..+..+.++....+++....+.+... .....+...+...++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIEDAGY 60 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHHcCC
Confidence 355 8899999999999999999887888887776666532 244444444455444
No 15
>PRK13748 putative mercuric reductase; Provisional
Probab=81.99 E-value=7 Score=41.06 Aligned_cols=64 Identities=17% Similarity=0.378 Sum_probs=49.2
Q ss_pred EEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEe--cCCHHHHHHHHHhcCCceeeCCC
Q 016666 39 VLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKG--DVAAETLIGKLEKNGKHAELWPE 102 (385)
Q Consensus 39 ~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG--~id~eeLikaIrKAGy~Aelv~e 102 (385)
.+.+. |+|..|..+++..+..++++..+.+++....+.+.. ..+...+...+...++..+.+..
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~ 69 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADA 69 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCc
Confidence 46677 999999999999999999999999999988877763 24556666666777776544433
No 16
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=79.88 E-value=9.1 Score=32.80 Aligned_cols=70 Identities=20% Similarity=0.244 Sum_probs=48.0
Q ss_pred cceEEEEEEe-eccHhHHHHHHHHHhcCCCceEEEE-----e--ccCcEEEEEe-cCCHHHHHHHHHhcCCceeeCCCC
Q 016666 34 KCKTWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKI-----D--LRQHKVVVKG-DVAAETLIGKLEKNGKHAELWPES 103 (385)
Q Consensus 34 k~qTv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~V-----D--la~~kVTVtG-~id~eeLikaIrKAGy~Aelv~e~ 103 (385)
...+++|.|. -+-.--.--+-+.|.+++||..|.+ | ..+-++||.| +++.++|.+.|+..|-.++.+.+-
T Consensus 4 ~iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSiDev 82 (97)
T COG1888 4 GIRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSIDEV 82 (97)
T ss_pred cceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeehhhh
Confidence 3456677776 4433334456667888888766544 3 3455566666 599999999999999988877653
No 17
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=76.41 E-value=13 Score=31.93 Aligned_cols=68 Identities=22% Similarity=0.326 Sum_probs=46.1
Q ss_pred cceEEEEEEe-eccHhHHHHHHHHHhcCCCceEEEE-----eccCcEE--EEEec-CCHHHHHHHHHhcCCceeeCCC
Q 016666 34 KCKTWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKI-----DLRQHKV--VVKGD-VAAETLIGKLEKNGKHAELWPE 102 (385)
Q Consensus 34 k~qTv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~V-----Dla~~kV--TVtG~-id~eeLikaIrKAGy~Aelv~e 102 (385)
..++++|.|. -+-. -.-.+-+.|.+++||..|.+ |..+..+ +|.|. ++.++|.++|++.|-.++.+.+
T Consensus 3 ~irRlVLDVlKP~~p-~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSIDe 79 (95)
T PF02680_consen 3 GIRRLVLDVLKPHEP-SIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSIDE 79 (95)
T ss_dssp SEEEEEEEEEEESSS--HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEEEE
T ss_pred ceeEEEEEeecCCCC-CHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEeeee
Confidence 3467778887 5333 34467788999999877655 4444444 44564 9999999999999998876654
No 18
>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=59.84 E-value=15 Score=28.39 Aligned_cols=33 Identities=15% Similarity=0.389 Sum_probs=22.3
Q ss_pred eEEEEEEeeccHhHH------HHHHHHHhcCCCceEEEE
Q 016666 36 KTWVLRVSIHCEGCK------RKVHKILTNIDGVYTTKI 68 (385)
Q Consensus 36 qTv~LkVeM~C~gCa------~kIEKaL~kL~GV~~V~V 68 (385)
.++.|.+.+...+|. ..|+++|+.++||.+|+|
T Consensus 34 ~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 34 GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 345666666666654 678889999999998875
No 19
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=50.07 E-value=26 Score=32.66 Aligned_cols=44 Identities=16% Similarity=0.334 Sum_probs=35.3
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeccCcE-------------------EEEE---ecCCHHHHHHHH
Q 016666 47 EGCKRKVHKILTNIDGVYTTKIDLRQHK-------------------VVVK---GDVAAETLIGKL 90 (385)
Q Consensus 47 ~gCa~kIEKaL~kL~GV~~V~VDla~~k-------------------VTVt---G~id~eeLikaI 90 (385)
.+|-+.++..+.+|+||.++.+-+.++. |.|+ ..++.++|+...
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f 75 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELF 75 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHH
Confidence 5788889999999999999999877664 5555 348888988855
No 20
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=47.96 E-value=62 Score=27.07 Aligned_cols=48 Identities=17% Similarity=0.227 Sum_probs=33.8
Q ss_pred ecc-HhHHHHHHHHHhcCCCceEEEEeccCcEEEEE-ecCCHHHHHHHHH
Q 016666 44 IHC-EGCKRKVHKILTNIDGVYTTKIDLRQHKVVVK-GDVAAETLIGKLE 91 (385)
Q Consensus 44 M~C-~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVt-G~id~eeLikaIr 91 (385)
.+| +.=...|.+.|..++|+.-...|...+|+.|+ ...+..+++..|.
T Consensus 12 V~~~Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 12 VQAKSERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred EEeChHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 344 34477899999999999877778888888876 3445555555444
No 21
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=39.52 E-value=67 Score=24.45 Aligned_cols=53 Identities=21% Similarity=0.144 Sum_probs=38.0
Q ss_pred EEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEE--ecCCHHHHHHHHHhcCCceeeC
Q 016666 39 VLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVK--GDVAAETLIGKLEKNGKHAELW 100 (385)
Q Consensus 39 ~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVt--G~id~eeLikaIrKAGy~Aelv 100 (385)
+|.+. +.|+...-++.++|.+++.= +.+.|. .......|...++..|+.+..+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 45666 89999999999999997443 233343 3355688999999999975444
No 22
>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=38.47 E-value=1.6e+02 Score=21.78 Aligned_cols=59 Identities=12% Similarity=0.172 Sum_probs=35.8
Q ss_pred EEEEe-eccHhHHHHHHHHHhcCCC-ceEEEEecc----CcEEEEEe-cCCHHHHHHHHHhcCCce
Q 016666 39 VLRVS-IHCEGCKRKVHKILTNIDG-VYTTKIDLR----QHKVVVKG-DVAAETLIGKLEKNGKHA 97 (385)
Q Consensus 39 ~LkVe-M~C~gCa~kIEKaL~kL~G-V~~V~VDla----~~kVTVtG-~id~eeLikaIrKAGy~A 97 (385)
+|.|. -...+...+|...|.+..- |..+..... ...++|.- ..+.+.+++.|++.||.+
T Consensus 3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~~~G~~v 68 (72)
T cd04883 3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLRRAGYEV 68 (72)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHHHCCCee
Confidence 45555 3445677778888766533 544443332 22234432 256679999999999975
No 23
>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=36.66 E-value=1.2e+02 Score=24.47 Aligned_cols=45 Identities=22% Similarity=0.250 Sum_probs=32.1
Q ss_pred hHHHHHHHHHhcCCCceEEEEeccCcEEEEE-ecCCHHHHHHHHHhc
Q 016666 48 GCKRKVHKILTNIDGVYTTKIDLRQHKVVVK-GDVAAETLIGKLEKN 93 (385)
Q Consensus 48 gCa~kIEKaL~kL~GV~~V~VDla~~kVTVt-G~id~eeLikaIrKA 93 (385)
.=...|.++|..++||.-...+-. +++.|+ ...+..++.+.|..+
T Consensus 15 ~~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~i 60 (79)
T PF03927_consen 15 ERLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDAI 60 (79)
T ss_dssp CCHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHHH
T ss_pred hhHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHHH
Confidence 345688999999999976667777 666665 456667776666543
No 24
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=36.36 E-value=94 Score=24.19 Aligned_cols=44 Identities=18% Similarity=0.299 Sum_probs=32.3
Q ss_pred HhcCCCceEEEEeccC-cEEEEEecCCHHHHHHHHHhcCCceeeCC
Q 016666 57 LTNIDGVYTTKIDLRQ-HKVVVKGDVAAETLIGKLEKNGKHAELWP 101 (385)
Q Consensus 57 L~kL~GV~~V~VDla~-~kVTVtG~id~eeLikaIrKAGy~Aelv~ 101 (385)
|..+++|..+..+-.. -++.|....+..+|+..|...|. +.-+.
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f~ 70 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDEETANELLQELIEKGI-IRSFE 70 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHHhCCC-eeEEE
Confidence 8888999988764433 34445556788999999999998 66443
No 25
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=36.12 E-value=68 Score=29.56 Aligned_cols=44 Identities=25% Similarity=0.384 Sum_probs=33.8
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeccCcE--------------EEEE---ecCCHHHHHHHH
Q 016666 47 EGCKRKVHKILTNIDGVYTTKIDLRQHK--------------VVVK---GDVAAETLIGKL 90 (385)
Q Consensus 47 ~gCa~kIEKaL~kL~GV~~V~VDla~~k--------------VTVt---G~id~eeLikaI 90 (385)
.+|-+-++..+.+++||.++.+-+.++. |.|+ ..++.++|+...
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f 68 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYL 68 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHH
Confidence 5788889999999999999999766543 3344 248888888866
No 26
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=35.05 E-value=2.4e+02 Score=34.30 Aligned_cols=8 Identities=0% Similarity=0.339 Sum_probs=3.1
Q ss_pred CCceEEEE
Q 016666 61 DGVYTTKI 68 (385)
Q Consensus 61 ~GV~~V~V 68 (385)
+.|..|-+
T Consensus 1256 ~~i~kV~m 1263 (1605)
T KOG0260|consen 1256 PDIFKVYM 1263 (1605)
T ss_pred cccceEEE
Confidence 33444333
No 27
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=34.43 E-value=62 Score=31.39 Aligned_cols=45 Identities=22% Similarity=0.319 Sum_probs=34.8
Q ss_pred cHhHHHHHHHHHhcCCCceEEEEeccCcE-------------------EEEEe---cCCHHHHHHHH
Q 016666 46 CEGCKRKVHKILTNIDGVYTTKIDLRQHK-------------------VVVKG---DVAAETLIGKL 90 (385)
Q Consensus 46 C~gCa~kIEKaL~kL~GV~~V~VDla~~k-------------------VTVtG---~id~eeLikaI 90 (385)
-.+|-+.++..+.+|+||.++.+-+.++. |.|+. .++.++|+..+
T Consensus 51 agGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~F 117 (213)
T PRK00058 51 GMGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVF 117 (213)
T ss_pred EccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHH
Confidence 46788888999999999999999877442 44443 48889988865
No 28
>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=34.22 E-value=52 Score=30.70 Aligned_cols=36 Identities=14% Similarity=0.308 Sum_probs=25.5
Q ss_pred EEEEEEeeccHhHH------HHHHHHHhcCCCceEEEEeccC
Q 016666 37 TWVLRVSIHCEGCK------RKVHKILTNIDGVYTTKIDLRQ 72 (385)
Q Consensus 37 Tv~LkVeM~C~gCa------~kIEKaL~kL~GV~~V~VDla~ 72 (385)
++.|.|.+...+|. ..|+.+|..++||..++|++..
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l~~ 155 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVELVF 155 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEEEe
Confidence 35555556655554 4488999999999998887643
No 29
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=33.15 E-value=2.1e+02 Score=23.57 Aligned_cols=59 Identities=17% Similarity=0.165 Sum_probs=43.7
Q ss_pred eEEEEEEeeccHhHHHHHHHHHhcCCC-ceEEEEeccCcEEEEEecCCHHHHHHHHHhcCC
Q 016666 36 KTWVLRVSIHCEGCKRKVHKILTNIDG-VYTTKIDLRQHKVVVKGDVAAETLIGKLEKNGK 95 (385)
Q Consensus 36 qTv~LkVeM~C~gCa~kIEKaL~kL~G-V~~V~VDla~~kVTVtG~id~eeLikaIrKAGy 95 (385)
.|+.=+|+-+=..+...+...|..... -..+.|+..++.|.|.|+. ..+|.+.|...||
T Consensus 28 ~T~IrkI~GD~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~-~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 28 ITVIRKIEGDIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGDH-VEEVKKWLLEKGF 87 (87)
T ss_pred EEEEEeecCCHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCcc-HHHHHHHHHHCcC
Confidence 344446664456777777777765544 2368899999999999985 7888999988887
No 30
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=32.64 E-value=52 Score=31.20 Aligned_cols=44 Identities=20% Similarity=0.340 Sum_probs=34.1
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeccCcE-------------------EEEE---ecCCHHHHHHHH
Q 016666 47 EGCKRKVHKILTNIDGVYTTKIDLRQHK-------------------VVVK---GDVAAETLIGKL 90 (385)
Q Consensus 47 ~gCa~kIEKaL~kL~GV~~V~VDla~~k-------------------VTVt---G~id~eeLikaI 90 (385)
.+|-+-++..+.+|+||..+.+-+.++. |.|+ ..++.++|+..+
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~F 80 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIF 80 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHH
Confidence 5677778889999999999999877664 4444 248889988865
No 31
>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=31.28 E-value=1.3e+02 Score=22.48 Aligned_cols=34 Identities=15% Similarity=0.173 Sum_probs=25.3
Q ss_pred ceEEEEEEeeccHh-HHHHHHHHHhcCCCceEEEE
Q 016666 35 CKTWVLRVSIHCEG-CKRKVHKILTNIDGVYTTKI 68 (385)
Q Consensus 35 ~qTv~LkVeM~C~g-Ca~kIEKaL~kL~GV~~V~V 68 (385)
..++.|.|...-.. ....|.+.|++++||.+|.+
T Consensus 40 ~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 40 RANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred eEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 34455666645554 88899999999999998864
No 32
>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=30.70 E-value=62 Score=26.49 Aligned_cols=23 Identities=17% Similarity=0.303 Sum_probs=18.1
Q ss_pred HHHHHHHhcCCCceEEEEeccCc
Q 016666 51 RKVHKILTNIDGVYTTKIDLRQH 73 (385)
Q Consensus 51 ~kIEKaL~kL~GV~~V~VDla~~ 73 (385)
..|+.+|..++||..+.|++...
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~~~ 80 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELVWD 80 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEEee
Confidence 35788899999999998887533
No 33
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=28.55 E-value=2.5e+02 Score=20.93 Aligned_cols=58 Identities=16% Similarity=0.067 Sum_probs=36.3
Q ss_pred EEEe-eccHhHHHHHHHHHhcCCC-ceEEEEeccCcEEE--EEecCCHHHHHHHHHhcCCcee
Q 016666 40 LRVS-IHCEGCKRKVHKILTNIDG-VYTTKIDLRQHKVV--VKGDVAAETLIGKLEKNGKHAE 98 (385)
Q Consensus 40 LkVe-M~C~gCa~kIEKaL~kL~G-V~~V~VDla~~kVT--VtG~id~eeLikaIrKAGy~Ae 98 (385)
|.|. -+..+=..+|-+.|.+... |..+-+.....+.+ +.. .+.+.+.+.|++.||++.
T Consensus 4 i~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~~~~~~rl~~-~~~~~~~~~L~~~G~~v~ 65 (66)
T cd04908 4 LSVFLENKPGRLAAVTEILSEAGINIRALSIADTSEFGILRLIV-SDPDKAKEALKEAGFAVK 65 (66)
T ss_pred EEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecCCCCEEEEEE-CCHHHHHHHHHHCCCEEE
Confidence 4455 4556677788888766543 44444433322333 334 567799999999999875
No 34
>PRK12757 cell division protein FtsN; Provisional
Probab=28.28 E-value=2.4e+02 Score=28.22 Aligned_cols=65 Identities=18% Similarity=0.267 Sum_probs=45.1
Q ss_pred cceEEEEEEe-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEE-ec----CCHHHHHHHHHhcCCceeeC
Q 016666 34 KCKTWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVK-GD----VAAETLIGKLEKNGKHAELW 100 (385)
Q Consensus 34 k~qTv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVt-G~----id~eeLikaIrKAGy~Aelv 100 (385)
....+.|.|. ..-...+.++...|.. .|+. +.|....+..+|. |- ...+.++..|+.+||...++
T Consensus 181 ~~~~~~VQVGAF~~~~nAe~L~arL~~-~G~~-a~I~~~gg~yRVrVGPf~sr~~A~~~~~rLk~~G~~~~ii 251 (256)
T PRK12757 181 KEQRWMVQCGSFKGTEQAESVRAQLAF-AGIE-SRITTGGGWNRVVLGPYNSKAAADKMLQRLKGAGHSGCIP 251 (256)
T ss_pred CCccEEEEEeeCCCHHHHHHHHHHHHh-cCCc-eEEeecCCEEEEEeCCCCCHHHHHHHHHHHHHcCCCCeEE
Confidence 3456788888 8899999999999974 5764 4454444555553 42 34577888889999965443
No 35
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=27.17 E-value=1.3e+02 Score=33.16 Aligned_cols=35 Identities=23% Similarity=0.321 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCCCC-CCCCCCCCCCCCcccccccccCC
Q 016666 291 ASYSPPRQHGYPYP-QYAPPPHYYTPPVYATSYNTAHP 327 (385)
Q Consensus 291 ~~~~pp~~~~~~~~-~y~~p~~yy~pp~y~~sy~ta~P 327 (385)
+..+|-.+.+++|+ .- -|.||-||....+-+|++|
T Consensus 592 ~~~~pg~pPpq~~q~l~--~ptyfvpP~qmt~g~~~~p 627 (694)
T KOG4264|consen 592 KRFVPGPPPPQVAQGLV--VPTYFVPPPQMTRGSTHGP 627 (694)
T ss_pred cccCCCCCCcccccccc--ccccccCccccccCCCCCC
Confidence 33344455556656 34 6788888888888888888
No 36
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=26.76 E-value=1.5e+02 Score=27.06 Aligned_cols=44 Identities=23% Similarity=0.373 Sum_probs=33.1
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeccCc-------------------EEEEE---ecCCHHHHHHHH
Q 016666 47 EGCKRKVHKILTNIDGVYTTKIDLRQH-------------------KVVVK---GDVAAETLIGKL 90 (385)
Q Consensus 47 ~gCa~kIEKaL~kL~GV~~V~VDla~~-------------------kVTVt---G~id~eeLikaI 90 (385)
.+|-+.++..+.+++||.++.+-+.++ .|.|+ ..++.++|+..+
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f 72 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVF 72 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHH
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHH
Confidence 478888999999999999999976654 23344 348888888876
No 37
>PRK11670 antiporter inner membrane protein; Provisional
Probab=25.02 E-value=2e+02 Score=29.54 Aligned_cols=66 Identities=18% Similarity=0.195 Sum_probs=42.3
Q ss_pred EEEEEEeeccHhH------HHHHHHHHhcCCCceEEEEeccC------------------cEEEEE------e-cCCHHH
Q 016666 37 TWVLRVSIHCEGC------KRKVHKILTNIDGVYTTKIDLRQ------------------HKVVVK------G-DVAAET 85 (385)
Q Consensus 37 Tv~LkVeM~C~gC------a~kIEKaL~kL~GV~~V~VDla~------------------~kVTVt------G-~id~ee 85 (385)
++.|.|.+.-..| ...++.+|..++||..+.|.+.. ..+.|. | ++...-
T Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avN 127 (369)
T PRK11670 48 TLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVN 127 (369)
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHH
Confidence 3445555433333 34688999999999877765432 223343 2 144566
Q ss_pred HHHHHHhcCCceeeCCC
Q 016666 86 LIGKLEKNGKHAELWPE 102 (385)
Q Consensus 86 LikaIrKAGy~Aelv~e 102 (385)
|..+|.+.|+++-++..
T Consensus 128 LA~aLA~~G~rVlLID~ 144 (369)
T PRK11670 128 LALALAAEGAKVGILDA 144 (369)
T ss_pred HHHHHHHCCCcEEEEeC
Confidence 77788999999887765
No 38
>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=23.48 E-value=2e+02 Score=25.84 Aligned_cols=59 Identities=5% Similarity=0.068 Sum_probs=40.8
Q ss_pred eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEe-----cCCHH----HHHHHHHhc--C-CceeeCCC
Q 016666 44 IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKG-----DVAAE----TLIGKLEKN--G-KHAELWPE 102 (385)
Q Consensus 44 M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG-----~id~e----eLikaIrKA--G-y~Aelv~e 102 (385)
..=..=+..|.+.|.+++||..+.|=.....+.|-- ..... +|.++|+++ + |.+.+..+
T Consensus 71 ~~~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~~~~~~~~~i~~~V~~~v~~~~p~~~~V~Vs~D 141 (177)
T PF09580_consen 71 NDRQQLADRIANRVKKVPGVEDATVVVTDDNAYVAVDLDFNRFNTKKIKKKVEKAVKSADPRIYNVYVSTD 141 (177)
T ss_pred chHHHHHHHHHHHHhcCCCceEEEEEEECCEEEEEEEecccccchhHHHHHHHHHHHHhCCCccEEEEEcC
Confidence 445567889999999999999999999888888742 23333 444555543 2 55665555
No 39
>KOG4730 consensus D-arabinono-1, 4-lactone oxidase [Defense mechanisms]
Probab=23.09 E-value=54 Score=35.46 Aligned_cols=68 Identities=21% Similarity=0.230 Sum_probs=48.1
Q ss_pred hccccccccceEEEEE--Ee-eccHhHHHHHHHHHhcCCCceEEEEeccCcEEEEEecCCHHHHHHHHHhcCCcee
Q 016666 26 AGENQEQLKCKTWVLR--VS-IHCEGCKRKVHKILTNIDGVYTTKIDLRQHKVVVKGDVAAETLIGKLEKNGKHAE 98 (385)
Q Consensus 26 ~~e~~~~~k~qTv~Lk--Ve-M~C~gCa~kIEKaL~kL~GV~~V~VDla~~kVTVtG~id~eeLikaIrKAGy~Ae 98 (385)
++...+..+++++.+- ++ |.|..- ..--|..+.-| +++|....+|||...+...+|+..|.+.|+...
T Consensus 67 a~A~~a~~kirvVg~gHSp~~l~ctdg---~lisl~~lnkV--v~~dpe~~tvTV~aGirlrQLie~~~~~GlsL~ 137 (518)
T KOG4730|consen 67 AAATEAGKKIRVVGSGHSPSKLVCTDG---LLISLDKLNKV--VEFDPELKTVTVQAGIRLRQLIEELAKLGLSLP 137 (518)
T ss_pred HHHHHcCceEEEecccCCCCcceeccc---cEEEhhhhccc--eeeCchhceEEeccCcCHHHHHHHHHhcCcccc
Confidence 3334555666666544 44 888765 33334555666 556888899999999999999999999999753
No 40
>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=22.99 E-value=3.2e+02 Score=20.19 Aligned_cols=59 Identities=17% Similarity=0.046 Sum_probs=34.5
Q ss_pred EEEEe-eccHhHHHHHHHHHhcCCC-ceEEEEecc----CcEEEEEe--cCCHHHHHHHHHhcCCce
Q 016666 39 VLRVS-IHCEGCKRKVHKILTNIDG-VYTTKIDLR----QHKVVVKG--DVAAETLIGKLEKNGKHA 97 (385)
Q Consensus 39 ~LkVe-M~C~gCa~kIEKaL~kL~G-V~~V~VDla----~~kVTVtG--~id~eeLikaIrKAGy~A 97 (385)
.|.|. -.=.+...+|.+.|.+..- |..+.+... ...+.+.- ..+.+.+++.|+++||.+
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~~~~~~~~~i~v~~~~~~~~~~~~L~~~G~~v 69 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQEDRERAKEILKEAGYEV 69 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEeecCCcEEEEEEECCHHHHHHHHHHHHHcCCcC
Confidence 34444 2334577778888866543 444433321 33344332 236789999999999963
No 41
>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=22.77 E-value=57 Score=24.20 Aligned_cols=31 Identities=19% Similarity=0.362 Sum_probs=15.4
Q ss_pred HHHHHHhc---CCCceEEEEeccCcEEEEEecCCH
Q 016666 52 KVHKILTN---IDGVYTTKIDLRQHKVVVKGDVAA 83 (385)
Q Consensus 52 kIEKaL~k---L~GV~~V~VDla~~kVTVtG~id~ 83 (385)
+|+..|.. +++. .+.|...++.|+|.|.++.
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~s 36 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGEVPS 36 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEEESS
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEeeCcH
Confidence 46666665 3444 5677788888888887543
No 42
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=22.26 E-value=2.3e+02 Score=21.80 Aligned_cols=35 Identities=17% Similarity=0.154 Sum_probs=27.0
Q ss_pred ccceEEEEEEeeccHhHHHHHHHHHhcCCCceEEE
Q 016666 33 LKCKTWVLRVSIHCEGCKRKVHKILTNIDGVYTTK 67 (385)
Q Consensus 33 ~k~qTv~LkVeM~C~gCa~kIEKaL~kL~GV~~V~ 67 (385)
.....+.|.|...-..-...|...|++++||..|.
T Consensus 45 ~~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 45 DGTARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp TTEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred CCEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 34556677777777777788999999999998764
No 43
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=22.24 E-value=1.8e+02 Score=26.84 Aligned_cols=42 Identities=17% Similarity=0.220 Sum_probs=32.0
Q ss_pred ceEEEEEEe-eccHhHHHHHHHHHhcCCCceEEEEecc-CcEEEE
Q 016666 35 CKTWVLRVS-IHCEGCKRKVHKILTNIDGVYTTKIDLR-QHKVVV 77 (385)
Q Consensus 35 ~qTv~LkVe-M~C~gCa~kIEKaL~kL~GV~~V~VDla-~~kVTV 77 (385)
-..+++.|+ -.|..|..-|...+++ -|+..+.|-.. ++++.+
T Consensus 99 g~~~tm~Vdr~vC~~C~~~i~~~a~~-lGl~~L~I~~~~sG~~~~ 142 (146)
T PF14437_consen 99 GRSMTMYVDRDVCGYCGGDIPSMAEK-LGLKSLTIHEPDSGKVYY 142 (146)
T ss_pred CCeEEEEECcccchHHHHHHHHHHHH-cCCCeEEEEecCCCcEEE
Confidence 356789999 9999999888877766 47877777666 665543
No 44
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=21.60 E-value=1.3e+02 Score=30.36 Aligned_cols=46 Identities=22% Similarity=0.347 Sum_probs=35.0
Q ss_pred ccHhHHHHHHHHHhcCCCceEEEEeccCcE-------------------EEEE---ecCCHHHHHHHH
Q 016666 45 HCEGCKRKVHKILTNIDGVYTTKIDLRQHK-------------------VVVK---GDVAAETLIGKL 90 (385)
Q Consensus 45 ~C~gCa~kIEKaL~kL~GV~~V~VDla~~k-------------------VTVt---G~id~eeLikaI 90 (385)
--.+|-+.++..+.+++||.++.+-+.++. |.|+ ..++.++|+..+
T Consensus 132 fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~isy~~LL~~F 199 (283)
T PRK05550 132 FAGGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKISYETLLKVF 199 (283)
T ss_pred EecCCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHH
Confidence 356788889999999999999999766553 4444 347888888866
No 45
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=20.62 E-value=4.2e+02 Score=30.98 Aligned_cols=8 Identities=38% Similarity=0.771 Sum_probs=4.5
Q ss_pred CCCCCCCC
Q 016666 274 SPMYGPHG 281 (385)
Q Consensus 274 ~~~~g~~~ 281 (385)
.|++|..|
T Consensus 548 PPlpggag 555 (1102)
T KOG1924|consen 548 PPLPGGAG 555 (1102)
T ss_pred CCCCCCCC
Confidence 55666544
No 46
>PRK07334 threonine dehydratase; Provisional
Probab=20.11 E-value=3.7e+02 Score=27.61 Aligned_cols=64 Identities=16% Similarity=0.159 Sum_probs=41.8
Q ss_pred EEEEEEe-eccHhHHHHHHHHHhcCCC-ceEEEEecc-----CcEEEEE------ecCCHHHHHHHHHhcCCceeeC
Q 016666 37 TWVLRVS-IHCEGCKRKVHKILTNIDG-VYTTKIDLR-----QHKVVVK------GDVAAETLIGKLEKNGKHAELW 100 (385)
Q Consensus 37 Tv~LkVe-M~C~gCa~kIEKaL~kL~G-V~~V~VDla-----~~kVTVt------G~id~eeLikaIrKAGy~Aelv 100 (385)
.+.|.|. ..=.+=...|...|.+... |.++.+... .+.+.+. .....+.|+..|++.||.++++
T Consensus 326 ~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr~~g~~~~~~ 402 (403)
T PRK07334 326 LARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALRAAGFEARLV 402 (403)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHHHcCCeeEeC
Confidence 3577777 6666678888888876532 555555422 3454432 1133568899999999998876
No 47
>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=20.04 E-value=4.5e+02 Score=20.87 Aligned_cols=64 Identities=14% Similarity=0.216 Sum_probs=41.1
Q ss_pred EEEEee-ccHhHHHHHHHHHhcCCCceEEEEec---cCcEEEEE-e----cCCHHHHHHHHHhcCCceeeCCCC
Q 016666 39 VLRVSI-HCEGCKRKVHKILTNIDGVYTTKIDL---RQHKVVVK-G----DVAAETLIGKLEKNGKHAELWPES 103 (385)
Q Consensus 39 ~LkVeM-~C~gCa~kIEKaL~kL~GV~~V~VDl---a~~kVTVt-G----~id~eeLikaIrKAGy~Aelv~e~ 103 (385)
+|.|.| .=++--.++-.+|. -..|..+..+. ....+.|. . ....++|++.|++.||.+....+.
T Consensus 3 vl~v~ipD~PG~L~~ll~~l~-~anI~~~~y~~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~~~~~ 75 (85)
T cd04906 3 LLAVTIPERPGSFKKFCELIG-PRNITEFNYRYADEKDAHIFVGVSVANGAEELAELLEDLKSAGYEVVDLSDD 75 (85)
T ss_pred EEEEecCCCCcHHHHHHHHhC-CCceeEEEEEccCCCeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEECCCC
Confidence 456663 44566667777777 34565555554 34444442 2 234789999999999998877664
Done!