Query psy14390
Match_columns 64
No_of_seqs 108 out of 729
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 18:39:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14390.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14390hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03949 Malic_M: Malic enzyme 99.3 4.4E-13 9.5E-18 95.6 2.1 43 1-44 48-90 (255)
2 KOG1257|consensus 99.3 1.5E-12 3.3E-17 100.9 2.9 43 1-43 333-375 (582)
3 cd05312 NAD_bind_1_malic_enz N 99.2 3.3E-12 7.2E-17 92.1 1.7 43 1-44 48-90 (279)
4 cd00762 NAD_bind_malic_enz NAD 99.2 1.3E-11 2.9E-16 88.1 2.9 42 1-43 48-92 (254)
5 PRK13529 malate dehydrogenase; 99.1 1.3E-11 2.9E-16 95.7 1.9 42 1-43 318-359 (563)
6 PTZ00317 NADP-dependent malic 99.1 1.9E-11 4.2E-16 94.8 2.3 43 1-43 320-362 (559)
7 PLN03129 NADP-dependent malic 99.0 1.3E-10 2.9E-15 90.5 1.9 40 4-43 348-387 (581)
8 PRK12861 malic enzyme; Reviewe 98.1 1.1E-06 2.3E-11 70.6 1.9 39 2-44 209-247 (764)
9 PRK12862 malic enzyme; Reviewe 98.0 1.9E-06 4.1E-11 68.9 1.7 38 3-44 214-251 (763)
10 PRK07232 bifunctional malic en 98.0 2.8E-06 6E-11 68.1 1.7 39 3-45 206-244 (752)
11 cd05311 NAD_bind_2_malic_enz N 97.0 0.0002 4.4E-09 49.4 0.6 37 3-43 46-82 (226)
12 COG0281 SfcA Malic enzyme [Ene 96.7 0.00066 1.4E-08 52.1 0.9 33 3-40 220-252 (432)
13 PHA02091 hypothetical protein 84.3 0.3 6.5E-06 29.3 -0.0 34 14-48 2-40 (72)
14 PLN02150 terpene synthase/cycl 69.0 2.2 4.8E-05 26.2 0.7 16 1-16 14-29 (96)
15 TIGR03781 Bac_Flav_CT_K Bacter 58.6 11 0.00024 26.5 2.6 15 9-24 38-52 (202)
16 TIGR03147 cyt_nit_nrfF cytochr 51.2 3.3 7.1E-05 27.2 -0.9 22 1-24 69-90 (126)
17 PRK10144 formate-dependent nit 44.0 5 0.00011 26.3 -0.8 24 1-26 69-92 (126)
18 KOG2423|consensus 41.4 15 0.00033 29.3 1.3 19 11-29 350-368 (572)
19 COG3707 AmiR Response regulato 38.0 9.7 0.00021 26.7 -0.2 15 1-15 155-169 (194)
20 PF03861 ANTAR: ANTAR domain; 31.2 8.1 0.00018 21.1 -1.2 15 1-15 23-37 (56)
21 COG0719 SufB Cysteine desulfur 27.2 31 0.00067 25.9 0.9 15 1-15 368-382 (412)
22 PF06755 DUF1219: Protein of u 25.6 7.7 0.00017 25.3 -2.2 42 2-46 53-95 (114)
23 PF00690 Cation_ATPase_N: Cati 23.3 37 0.0008 18.8 0.6 19 3-21 18-36 (69)
24 PHA00447 lysozyme 23.2 60 0.0013 21.0 1.6 15 16-30 47-61 (142)
25 smart00701 PGRP Animal peptido 22.4 65 0.0014 20.8 1.6 15 16-30 67-81 (142)
26 PF04134 DUF393: Protein of un 22.1 75 0.0016 18.7 1.8 25 3-28 42-67 (114)
27 TIGR01261 hisB_Nterm histidino 21.9 60 0.0013 21.1 1.4 15 13-27 1-15 (161)
28 PF02617 ClpS: ATP-dependent C 21.7 11 0.00024 22.0 -1.9 20 5-24 31-50 (82)
29 PF00578 AhpC-TSA: AhpC/TSA fa 21.2 77 0.0017 18.3 1.7 15 11-25 108-122 (124)
30 KOG3220|consensus 20.3 37 0.00081 24.4 0.2 15 1-15 144-158 (225)
31 PF01563 Alpha_E3_glycop: Alph 20.1 79 0.0017 18.2 1.5 20 44-63 30-49 (56)
No 1
>PF03949 Malic_M: Malic enzyme, NAD binding domain; InterPro: IPR012302 Malic enzymes (malate oxidoreductases) catalyse the oxidative decarboxylation of malate to form pyruvate [], a reaction important in a number of metabolic pathways - e.g. carbon dioxide released from the reaction may be used in sugar production during the Calvin cycle of photosynthesis []. There are 3 forms of the enzyme []: an NAD-dependent form that decarboxylates oxaloacetate; an NAD-dependent form that does not decarboxylate oxalo-acetate; and an NADPH-dependent form []. Other proteins known to be similar to malic enzymes are the Escherichia coli scfA protein; an enzyme from Zea mays (Maize), formerly thought to be cinnamyl-alcohol dehydrogenase []; and the hypothetical Saccharomyces cerevisiae protein YKL029c. Studies on the duck liver malic enzyme reveals that it can be alkylated by bromopyruvate, resulting in the loss of oxidative decarboxylation and the subsequent enhancement of pyruvate reductase activity []. The alkylated form is able to bind NADPH but not L-malate, indicating impaired substrate-or divalent metal ion-binding in the active site []. Sequence analysis has highlighted a cysteine residue as the point of alkylation, suggesting that it may play an important role in the activity of the enzyme [], although it is absent in the sequences from some species. There are three well conserved regions in the enzyme sequences. Two of them seem to be involved in the binding NAD or NADP. The significance of the third one, located in the central part of the enzymes, is not yet known.; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 2DVM_B 1WW8_A 3NV9_A 1PJ2_A 1PJL_B 1GZ3_A 1PJ4_A 1PJ3_C 1EFL_A 1EFK_B ....
Probab=99.33 E-value=4.4e-13 Score=95.61 Aligned_cols=43 Identities=35% Similarity=0.611 Sum_probs=39.0
Q ss_pred CccCCCCHHHHhcceeEEecCCceecCCCCCCChhhhccccccc
Q psy14390 1 MQTEGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKYYSLIQE 44 (64)
Q Consensus 1 m~~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~FAr~~~ 44 (64)
|+++|+|++||++||||+|++|||+++|++ ++++|++||++..
T Consensus 48 ~~~~G~~~~eA~~~i~lvD~~Gll~~~r~~-l~~~~~~~a~~~~ 90 (255)
T PF03949_consen 48 MVREGLSEEEARKRIWLVDSKGLLTDDRED-LNPHKKPFARKTN 90 (255)
T ss_dssp HHCTTS-HHHHHTTEEEEETTEEEBTTTSS-HSHHHHHHHBSSS
T ss_pred HHHhcCCHHHHhccEEEEeccceEeccCcc-CChhhhhhhccCc
Confidence 567899999999999999999999999988 9999999999763
No 2
>KOG1257|consensus
Probab=99.28 E-value=1.5e-12 Score=100.94 Aligned_cols=43 Identities=35% Similarity=0.622 Sum_probs=39.8
Q ss_pred CccCCCCHHHHhcceeEEecCCceecCCCCCCChhhhcccccc
Q psy14390 1 MQTEGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKYYSLIQ 43 (64)
Q Consensus 1 m~~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~FAr~~ 43 (64)
|+++|+|+|||+++|||||++|||+++|+.+++++|++||+++
T Consensus 333 m~~~Gl~~eeA~kkIwlvD~~GLi~~~r~~~l~~~~~~fAk~~ 375 (582)
T KOG1257|consen 333 MVKEGLSEEEARKKIWLVDSKGLITKGRKASLTEEKKPFAKDH 375 (582)
T ss_pred HHHcCCCHHHHhccEEEEecCceeeccccCCCChhhccccccC
Confidence 5678999999999999999999999999844999999999976
No 3
>cd05312 NAD_bind_1_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 1. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists of eukaryotic and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH
Probab=99.22 E-value=3.3e-12 Score=92.06 Aligned_cols=43 Identities=37% Similarity=0.608 Sum_probs=39.7
Q ss_pred CccCCCCHHHHhcceeEEecCCceecCCCCCCChhhhccccccc
Q psy14390 1 MQTEGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKYYSLIQE 44 (64)
Q Consensus 1 m~~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~FAr~~~ 44 (64)
|+++|+|+|||+++|||+|++|||+++|++ ++++|++||++.+
T Consensus 48 ~~~~G~~~eeA~~~i~~vD~~Gll~~~r~~-l~~~~~~~a~~~~ 90 (279)
T cd05312 48 MVREGLSEEEARKKIWLVDSKGLLTKDRKD-LTPFKKPFARKDE 90 (279)
T ss_pred HHHcCCChhhccCeEEEEcCCCeEeCCCCc-chHHHHHHHhhcC
Confidence 456799999999999999999999999998 9999999999754
No 4
>cd00762 NAD_bind_malic_enz NAD(P) binding domain of malic enzyme. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glut
Probab=99.18 E-value=1.3e-11 Score=88.06 Aligned_cols=42 Identities=36% Similarity=0.458 Sum_probs=38.6
Q ss_pred CccCCCCHHHHhcceeEEecCCceecCCCCCCChhhhc---ccccc
Q psy14390 1 MQTEGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKY---YSLIQ 43 (64)
Q Consensus 1 m~~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~---FAr~~ 43 (64)
|+++|+|+|||++|||++|++|||+++|++ ++++|++ |+++.
T Consensus 48 ~~~~Gls~e~A~~~i~~vD~~Gll~~~r~~-l~~~~~~~~~~~~~~ 92 (254)
T cd00762 48 XVKEGISKEEACKRIWXVDRKGLLVKNRKE-TCPNEYHLARFANPE 92 (254)
T ss_pred HHhcCCCHHHHhccEEEECCCCeEeCCCCc-cCHHHHHHHHHcCcc
Confidence 356799999999999999999999999998 9999999 88874
No 5
>PRK13529 malate dehydrogenase; Provisional
Probab=99.15 E-value=1.3e-11 Score=95.73 Aligned_cols=42 Identities=33% Similarity=0.465 Sum_probs=39.4
Q ss_pred CccCCCCHHHHhcceeEEecCCceecCCCCCCChhhhcccccc
Q psy14390 1 MQTEGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKYYSLIQ 43 (64)
Q Consensus 1 m~~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~FAr~~ 43 (64)
|+++|+|+|||+++|||+|++|||+++|++ |+++|++||++.
T Consensus 318 ~~~~Gl~~eeA~~~i~~vD~~GLl~~~r~~-l~~~k~~fa~~~ 359 (563)
T PRK13529 318 MVREGLSEEEARKRFFMVDRQGLLTDDMPD-LLDFQKPYARKR 359 (563)
T ss_pred HHHcCCChhHhcCeEEEEcCCCeEeCCCCc-chHHHHHHhhhc
Confidence 456899999999999999999999999998 999999999975
No 6
>PTZ00317 NADP-dependent malic enzyme; Provisional
Probab=99.13 E-value=1.9e-11 Score=94.82 Aligned_cols=43 Identities=19% Similarity=0.275 Sum_probs=39.3
Q ss_pred CccCCCCHHHHhcceeEEecCCceecCCCCCCChhhhcccccc
Q psy14390 1 MQTEGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKYYSLIQ 43 (64)
Q Consensus 1 m~~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~FAr~~ 43 (64)
|+++|+|+|||++||||+|++|||+++|.++++++|++||++.
T Consensus 320 m~~~Gls~eeA~~~i~~vD~~GLl~~~r~~~l~~~k~~fa~~~ 362 (559)
T PTZ00317 320 AAEYGVTREEALKSFYLVDSKGLVTTTRGDKLAKHKVPFARTD 362 (559)
T ss_pred HHHcCCChhHhcCeEEEEcCCCeEeCCCCccccHHHHHHhccc
Confidence 4568999999999999999999999999755999999999974
No 7
>PLN03129 NADP-dependent malic enzyme; Provisional
Probab=99.00 E-value=1.3e-10 Score=90.50 Aligned_cols=40 Identities=33% Similarity=0.572 Sum_probs=37.4
Q ss_pred CCCCHHHHhcceeEEecCCceecCCCCCCChhhhcccccc
Q psy14390 4 EGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKYYSLIQ 43 (64)
Q Consensus 4 ~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~FAr~~ 43 (64)
+|+|+|||++||||+|++|||+++|+++++++|++||++.
T Consensus 348 ~Gls~eeA~~~i~~vD~~GLi~~~r~~~l~~~k~~fa~~~ 387 (581)
T PLN03129 348 TGISEEEARKRIWLVDSKGLVTKSRKDSLQPFKKPFAHDH 387 (581)
T ss_pred cCCChhhhcCcEEEEcCCCeEeCCCCccChHHHHHHHhhc
Confidence 5999999999999999999999999765999999999974
No 8
>PRK12861 malic enzyme; Reviewed
Probab=98.13 E-value=1.1e-06 Score=70.58 Aligned_cols=39 Identities=23% Similarity=0.555 Sum_probs=33.8
Q ss_pred ccCCCCHHHHhcceeEEecCCceecCCCCCCChhhhccccccc
Q psy14390 2 QTEGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKYYSLIQE 44 (64)
Q Consensus 2 ~~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~FAr~~~ 44 (64)
+..|++++ ||||+|++|||+++|++.++++|++||++.+
T Consensus 209 ~~~G~~~~----~i~~~D~~Gli~~~r~~~l~~~k~~~a~~~~ 247 (764)
T PRK12861 209 VDLGLPVE----NIWVTDIEGVVYRGRTTLMDPDKERFAQETD 247 (764)
T ss_pred HHcCCChh----hEEEEcCCCeeeCCCcccCCHHHHHHHhhcC
Confidence 45688865 9999999999999997658999999999864
No 9
>PRK12862 malic enzyme; Reviewed
Probab=98.04 E-value=1.9e-06 Score=68.93 Aligned_cols=38 Identities=26% Similarity=0.531 Sum_probs=33.1
Q ss_pred cCCCCHHHHhcceeEEecCCceecCCCCCCChhhhccccccc
Q psy14390 3 TEGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKYYSLIQE 44 (64)
Q Consensus 3 ~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~FAr~~~ 44 (64)
..|+++ +||||+|++|||+++|++.++++|++||++.+
T Consensus 214 ~~G~~~----~~i~~~D~~G~i~~~r~~~l~~~~~~~a~~~~ 251 (763)
T PRK12862 214 SLGVKR----ENIWVTDIKGVVYEGRTELMDPWKARYAQKTD 251 (763)
T ss_pred HcCCCc----ccEEEEcCCCeeeCCCCccccHHHHHHhhhcc
Confidence 468774 89999999999999997559999999999754
No 10
>PRK07232 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed
Probab=97.99 E-value=2.8e-06 Score=68.10 Aligned_cols=39 Identities=23% Similarity=0.369 Sum_probs=33.1
Q ss_pred cCCCCHHHHhcceeEEecCCceecCCCCCCChhhhcccccccc
Q psy14390 3 TEGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKYYSLIQEL 45 (64)
Q Consensus 3 ~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~FAr~~~~ 45 (64)
..|++ ++||||+|++|||+++|+++++++|++||++.+.
T Consensus 206 ~~G~~----~~~i~~~D~~G~i~~~r~~~~~~~k~~~a~~~~~ 244 (752)
T PRK07232 206 ALGAK----KENIIVCDSKGVIYKGRTEGMDEWKAAYAVDTDA 244 (752)
T ss_pred HcCCC----cccEEEEcCCCeecCCCcccccHHHHHHhccCCC
Confidence 45777 6899999999999999954499999999997543
No 11
>cd05311 NAD_bind_2_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 2. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists primarily of archaeal and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydroph
Probab=97.02 E-value=0.0002 Score=49.42 Aligned_cols=37 Identities=16% Similarity=0.301 Sum_probs=30.6
Q ss_pred cCCCCHHHHhcceeEEecCCceecCCCCCCChhhhcccccc
Q psy14390 3 TEGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKYYSLIQ 43 (64)
Q Consensus 3 ~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~FAr~~ 43 (64)
..|++ +++||++|++||++.+|.++|.++|++|+++.
T Consensus 46 ~~G~~----~~~i~ivdr~gl~~~~r~~~L~~~~~~la~~~ 82 (226)
T cd05311 46 AAGAK----PENIVVVDSKGVIYEGREDDLNPDKNEIAKET 82 (226)
T ss_pred HcCcC----cceEEEEeCCCccccccchhhhHHHHHHHHHh
Confidence 34666 67999999999999998655899999998864
No 12
>COG0281 SfcA Malic enzyme [Energy production and conversion]
Probab=96.65 E-value=0.00066 Score=52.08 Aligned_cols=33 Identities=33% Similarity=0.575 Sum_probs=24.5
Q ss_pred cCCCCHHHHhcceeEEecCCceecCCCCCCChhhhccc
Q psy14390 3 TEGSTVQEARDRIWMMDIDGLLAKGRVEVVRGNGKYYS 40 (64)
Q Consensus 3 ~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~~~q~~FA 40 (64)
..|+.+ +||||+|++|+|+++|++ +...|..|+
T Consensus 220 ~~g~~~----~~i~~~D~~G~l~~~r~~-~~~~~~k~~ 252 (432)
T COG0281 220 AAGVKE----ENIFVVDRKGLLYDGRED-LTMNQKKYA 252 (432)
T ss_pred HhCCCc----ccEEEEecCCcccCCCcc-cccchHHHH
Confidence 345554 899999999999999987 544444443
No 13
>PHA02091 hypothetical protein
Probab=84.27 E-value=0.3 Score=29.26 Aligned_cols=34 Identities=18% Similarity=0.335 Sum_probs=26.6
Q ss_pred ceeEEecCCceecCCCCCCChhh-----hccccccccccc
Q psy14390 14 RIWMMDIDGLLAKGRVEVVRGNG-----KYYSLIQELNLN 48 (64)
Q Consensus 14 rI~lvDr~GLlt~~R~d~L~~~q-----~~FAr~~~~~~~ 48 (64)
+|-++|.+|.|...|.+ ..+++ ..||+-+++-++
T Consensus 2 ~irlid~kgfid~~r~~-~~~y~larsiv~fak~r~l~ii 40 (72)
T PHA02091 2 KIRLIDEKGFIDHCRKN-IVDYKLARSIVDFAKTRELQII 40 (72)
T ss_pred ceEEeccccchhhhhhh-hHHHHHHHHHHHHHhhheEEEE
Confidence 57899999999999987 55555 678887776643
No 14
>PLN02150 terpene synthase/cyclase family protein
Probab=69.04 E-value=2.2 Score=26.23 Aligned_cols=16 Identities=31% Similarity=0.387 Sum_probs=13.9
Q ss_pred CccCCCCHHHHhccee
Q psy14390 1 MQTEGSTVQEARDRIW 16 (64)
Q Consensus 1 m~~~Gls~eeArkrI~ 16 (64)
|.+.|+|+|||++.|-
T Consensus 14 Mke~g~seeeA~~~i~ 29 (96)
T PLN02150 14 MKQHGVTKEEAVSELK 29 (96)
T ss_pred hccCCCCHHHHHHHHH
Confidence 6778999999999884
No 15
>TIGR03781 Bac_Flav_CT_K Bacteroides conjugative transposon TraK protein. Members of this protein family are designated TraK and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage. PSI-BLAST reveals a distant relationship to proteins TrbF and VirB8 in Proteobacterial conjugal transfer systems.
Probab=58.60 E-value=11 Score=26.47 Aligned_cols=15 Identities=27% Similarity=0.583 Sum_probs=12.2
Q ss_pred HHHhcceeEEecCCce
Q psy14390 9 QEARDRIWMMDIDGLL 24 (64)
Q Consensus 9 eeArkrI~lvDr~GLl 24 (64)
++++++||++|. |=.
T Consensus 38 ~~sr~kIYVvD~-G~~ 52 (202)
T TIGR03781 38 EAQRKKIYVLDN-GKS 52 (202)
T ss_pred hhhcceEEEEcC-Ccc
Confidence 678999999998 633
No 16
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=51.16 E-value=3.3 Score=27.17 Aligned_cols=22 Identities=32% Similarity=0.357 Sum_probs=16.5
Q ss_pred CccCCCCHHHHhcceeEEecCCce
Q psy14390 1 MQTEGSTVQEARDRIWMMDIDGLL 24 (64)
Q Consensus 1 m~~~Gls~eeArkrI~lvDr~GLl 24 (64)
|+++|.|++|..+ ||++++|=-
T Consensus 69 ~i~~G~Sd~eI~~--~~v~RYG~~ 90 (126)
T TIGR03147 69 MVNEGKSNQQIID--FMTARFGDF 90 (126)
T ss_pred HHHcCCCHHHHHH--HHHHhcCCe
Confidence 4577888888776 788888844
No 17
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=44.03 E-value=5 Score=26.34 Aligned_cols=24 Identities=29% Similarity=0.488 Sum_probs=17.3
Q ss_pred CccCCCCHHHHhcceeEEecCCceec
Q psy14390 1 MQTEGSTVQEARDRIWMMDIDGLLAK 26 (64)
Q Consensus 1 m~~~Gls~eeArkrI~lvDr~GLlt~ 26 (64)
|+.+|.|++|... ||++++|=-.-
T Consensus 69 ~i~~G~sd~eI~~--~~v~RYG~~Vl 92 (126)
T PRK10144 69 MVAEGKSEVEIIG--WMTERYGDFVR 92 (126)
T ss_pred HHHcCCCHHHHHH--HHHHhcCCeEE
Confidence 4577889888776 78888884433
No 18
>KOG2423|consensus
Probab=41.43 E-value=15 Score=29.28 Aligned_cols=19 Identities=21% Similarity=0.401 Sum_probs=16.0
Q ss_pred HhcceeEEecCCceecCCC
Q psy14390 11 ARDRIWMMDIDGLLAKGRV 29 (64)
Q Consensus 11 ArkrI~lvDr~GLlt~~R~ 29 (64)
-.+|||++|+.|++.-+++
T Consensus 350 LmkrIfLIDcPGvVyps~d 368 (572)
T KOG2423|consen 350 LMKRIFLIDCPGVVYPSSD 368 (572)
T ss_pred HHhceeEecCCCccCCCCC
Confidence 3589999999999987763
No 19
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=37.96 E-value=9.7 Score=26.74 Aligned_cols=15 Identities=27% Similarity=0.381 Sum_probs=12.4
Q ss_pred CccCCCCHHHHhcce
Q psy14390 1 MQTEGSTVQEARDRI 15 (64)
Q Consensus 1 m~~~Gls~eeArkrI 15 (64)
|.+.|+|++||.+.+
T Consensus 155 M~~~g~sE~EAy~~l 169 (194)
T COG3707 155 MKRRGLSEEEAYKLL 169 (194)
T ss_pred HHHhCCCHHHHHHHH
Confidence 567899999998754
No 20
>PF03861 ANTAR: ANTAR domain; InterPro: IPR005561 ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins []. This domain has been detected in various response regulators of two-component systems, which are structured around two proteins, a histidine kinase and a response regulator. This domain is also found in one-component sensory regulators from a variety of bacteria. Most response regulators interact with DNA, however ANTAR-containing regulators interact with RNA. The majority of the domain consists of a coiled-coil.; PDB: 4AKK_A 1SD5_A 1S8N_A 1QO0_E.
Probab=31.24 E-value=8.1 Score=21.13 Aligned_cols=15 Identities=27% Similarity=0.240 Sum_probs=8.6
Q ss_pred CccCCCCHHHHhcce
Q psy14390 1 MQTEGSTVQEARDRI 15 (64)
Q Consensus 1 m~~~Gls~eeArkrI 15 (64)
|...|+|+++|...+
T Consensus 23 m~~~g~~e~~A~~~L 37 (56)
T PF03861_consen 23 MARYGLSEDEAYRLL 37 (56)
T ss_dssp HHHHT--HHHHHHHH
T ss_pred HHHhCcCHHHHHHHH
Confidence 345688888887643
No 21
>COG0719 SufB Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]
Probab=27.23 E-value=31 Score=25.95 Aligned_cols=15 Identities=27% Similarity=0.439 Sum_probs=12.3
Q ss_pred CccCCCCHHHHhcce
Q psy14390 1 MQTEGSTVQEARDRI 15 (64)
Q Consensus 1 m~~~Gls~eeArkrI 15 (64)
|++.|+|++||++=|
T Consensus 368 LmSRGl~e~eA~~lI 382 (412)
T COG0719 368 LMSRGLSEEEAKRLI 382 (412)
T ss_pred hhhcCCCHHHHHHHH
Confidence 567899999998754
No 22
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=25.56 E-value=7.7 Score=25.31 Aligned_cols=42 Identities=12% Similarity=0.142 Sum_probs=31.6
Q ss_pred ccCCCCHHHHhcceeEEecCCceecCCCCCCC-hhhhccccccccc
Q psy14390 2 QTEGSTVQEARDRIWMMDIDGLLAKGRVEVVR-GNGKYYSLIQELN 46 (64)
Q Consensus 2 ~~~Gls~eeArkrI~lvDr~GLlt~~R~d~L~-~~q~~FAr~~~~~ 46 (64)
++.|+|.-+|-+ ++||++.|+.-++.+ .+ ..|.||...-++-
T Consensus 53 idaGIs~~~AVN--~LVeKY~LvRiD~~g-Fs~~~qsP~l~~~Dil 95 (114)
T PF06755_consen 53 IDAGISPADAVN--FLVEKYELVRIDRNG-FSWQEQSPYLTAIDIL 95 (114)
T ss_pred HHhCCCHHHHHH--HHHHHHhhhhcCCcc-cCccCCCchhhHHHHH
Confidence 357999999887 579999999888876 54 4678887755443
No 23
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=23.32 E-value=37 Score=18.75 Aligned_cols=19 Identities=16% Similarity=0.241 Sum_probs=13.4
Q ss_pred cCCCCHHHHhcceeEEecC
Q psy14390 3 TEGSTVQEARDRIWMMDID 21 (64)
Q Consensus 3 ~~Gls~eeArkrI~lvDr~ 21 (64)
..|+|.+||.+|.=-...+
T Consensus 18 ~~GLs~~ev~~r~~~~G~N 36 (69)
T PF00690_consen 18 SQGLSSEEVEERRKKYGPN 36 (69)
T ss_dssp SSBBTHHHHHHHHHHHSSS
T ss_pred CCCCCHHHHHHHHHhcccc
Confidence 5699999998887443333
No 24
>PHA00447 lysozyme
Probab=23.16 E-value=60 Score=21.03 Aligned_cols=15 Identities=33% Similarity=0.711 Sum_probs=13.4
Q ss_pred eEEecCCceecCCCC
Q psy14390 16 WMMDIDGLLAKGRVE 30 (64)
Q Consensus 16 ~lvDr~GLlt~~R~d 30 (64)
|+||.+|-|.++|+.
T Consensus 47 f~I~~dG~I~eGR~~ 61 (142)
T PHA00447 47 FIIRRDGTVEEGRPE 61 (142)
T ss_pred EEECCCCEEEECCCC
Confidence 789999999999964
No 25
>smart00701 PGRP Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. The bacteriophage molecule, but not its moth homologue, has been shown to have N-acetylmuramoyl-L-alanine amidase activity. One member of this family, Tag7, is a cytokine.
Probab=22.40 E-value=65 Score=20.75 Aligned_cols=15 Identities=27% Similarity=0.386 Sum_probs=13.5
Q ss_pred eEEecCCceecCCCC
Q psy14390 16 WMMDIDGLLAKGRVE 30 (64)
Q Consensus 16 ~lvDr~GLlt~~R~d 30 (64)
|+||.+|-|.++|..
T Consensus 67 flI~~dG~IyeGR~~ 81 (142)
T smart00701 67 FLVGGDGKVYEGRGW 81 (142)
T ss_pred EEEcCCCEEEECCCC
Confidence 799999999999963
No 26
>PF04134 DUF393: Protein of unknown function, DUF393; InterPro: IPR007263 The DCC family, named after the conserved N-terminal DxxCxxC motif, encompasses COG3011 from COG. Proteins in this family are predicted to have a thioredoxin-like fold which, together with the presence of an invariant catalytic cysteine residue, suggests that they are a novel group of thiol-disulphide oxidoreductases []. As some of the bacterial proteins are encoded near penicillin-binding proteins, it has been suggested that these may be involved in redox regulation of cell wall biosynthesis [].
Probab=22.06 E-value=75 Score=18.74 Aligned_cols=25 Identities=24% Similarity=0.393 Sum_probs=19.0
Q ss_pred cCCCCHHHHhcceeEEecCCc-eecCC
Q psy14390 3 TEGSTVQEARDRIWMMDIDGL-LAKGR 28 (64)
Q Consensus 3 ~~Gls~eeArkrI~lvDr~GL-lt~~R 28 (64)
..|++.|++.+.+++ +.+|= +..+.
T Consensus 42 ~~~~~~~~~~~~l~~-~~~g~~~~~G~ 67 (114)
T PF04134_consen 42 SYGISPEDADSRLHL-IDDGERVYRGS 67 (114)
T ss_pred hcCcCHHHHcCeeEE-ecCCCEEEEcH
Confidence 358999999999999 66664 55554
No 27
>TIGR01261 hisB_Nterm histidinol-phosphatase. This model describes histidinol phosphatase. All known examples in the scope of this model are bifunctional proteins with a histidinol phosphatase domain followed by an imidazoleglycerol-phosphate dehydratase domain. These enzymatic domains catalyze the ninth and seventh steps, respectively, of histidine biosynthesis.
Probab=21.88 E-value=60 Score=21.05 Aligned_cols=15 Identities=33% Similarity=0.598 Sum_probs=12.3
Q ss_pred cceeEEecCCceecC
Q psy14390 13 DRIWMMDIDGLLAKG 27 (64)
Q Consensus 13 krI~lvDr~GLlt~~ 27 (64)
++|-++|++|.|.+.
T Consensus 1 ~~~~~~d~dg~l~~~ 15 (161)
T TIGR01261 1 QKILFIDRDGTLIEE 15 (161)
T ss_pred CCEEEEeCCCCcccc
Confidence 368899999999773
No 28
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=21.72 E-value=11 Score=21.95 Aligned_cols=20 Identities=20% Similarity=0.285 Sum_probs=15.1
Q ss_pred CCCHHHHhcceeEEecCCce
Q psy14390 5 GSTVQEARDRIWMMDIDGLL 24 (64)
Q Consensus 5 Gls~eeArkrI~lvDr~GLl 24 (64)
|+|.++|.+-.+-+|+.|--
T Consensus 31 ~~s~~~A~~~a~~v~~~G~a 50 (82)
T PF02617_consen 31 GCSEEQARQIAMEVHREGRA 50 (82)
T ss_dssp ---HHHHHHHHHHHHHHSEE
T ss_pred CCCHHHHHHHHHHHhHcCCE
Confidence 89999999999999999864
No 29
>PF00578 AhpC-TSA: AhpC/TSA family; InterPro: IPR000866 Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerisation states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidised to a sulphenic acid by the peroxide substrate. The recycling of the sulphenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity []. Alkyl hydroperoxide reductase (AhpC) is responsible for directly reducing organic hyperoxides in its reduced dithiol form. Thiol specific antioxidant (TSA) is a physiologically important antioxidant which constitutes an enzymatic defence against sulphur-containing radicals. This family contains AhpC and TSA, as well as related proteins.; GO: 0016209 antioxidant activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QMV_A 1PRX_B 3HJP_C 3HA9_A 2V41_G 2V32_C 2V2G_C 3LWA_A 3IA1_B 1ZYE_G ....
Probab=21.24 E-value=77 Score=18.30 Aligned_cols=15 Identities=27% Similarity=0.543 Sum_probs=11.9
Q ss_pred HhcceeEEecCCcee
Q psy14390 11 ARDRIWMMDIDGLLA 25 (64)
Q Consensus 11 ArkrI~lvDr~GLlt 25 (64)
+...+|++|++|-|.
T Consensus 108 ~~p~~~lid~~g~I~ 122 (124)
T PF00578_consen 108 ALPAVFLIDPDGKIR 122 (124)
T ss_dssp ESEEEEEEETTSBEE
T ss_pred eEeEEEEECCCCEEE
Confidence 445789999999884
No 30
>KOG3220|consensus
Probab=20.28 E-value=37 Score=24.45 Aligned_cols=15 Identities=13% Similarity=0.432 Sum_probs=12.1
Q ss_pred CccCCCCHHHHhcce
Q psy14390 1 MQTEGSTVQEARDRI 15 (64)
Q Consensus 1 m~~~Gls~eeArkrI 15 (64)
|.+.|+|+++|++|+
T Consensus 144 ~~Rd~lse~dAe~Rl 158 (225)
T KOG3220|consen 144 VERDELSEEDAENRL 158 (225)
T ss_pred HHhccccHHHHHHHH
Confidence 346789999999886
No 31
>PF01563 Alpha_E3_glycop: Alphavirus E3 glycoprotein; InterPro: IPR002533 Alphaviruses are enveloped RNA viruses that use arthropods such as mosquitoes for transmission to their vertebrate hosts, and include Semliki Forest and Sindbis viruses []. Alphaviruses consist of three structural proteins: the core nucleocapsid protein C, and the envelope proteins P62 and E1 (IPR002548 from INTERPRO) that associate as a heterodimer. The viral membrane-anchored surface glycoproteins are responsible for receptor recognition and entry into target cells through membrane fusion. The proteolytic maturation of P62 into E2 (IPR000936 from INTERPRO) and E3 causes a change in the viral surface. Together the E1, E2, and sometimes E3 glycoprotein "spikes" form an E1/E2 dimer or an E1/E2/E3 trimer, where E2 extends from the centre to the vertices, E1 fills the space between the vertices, and E3, if present, is at the distal end of the spike [, ]. Upon exposure of the virus to the acidity of the endosome, E1 dissociates from E2 to form an E1 homotrimer, which is necessary for the fusion step to drive the cellular and viral membranes together []. This entry represents the alphaviral E3 glycoprotein. Most alphaviruses lose the peripheral protein E3, but in Semliki viruses it remains associated with the viral surface.; GO: 0004252 serine-type endopeptidase activity, 0019028 viral capsid, 0055036 virion membrane; PDB: 3J0C_H 3J0G_N 3N40_P 3N41_A 3N44_A 3N42_A 3N43_A.
Probab=20.05 E-value=79 Score=18.24 Aligned_cols=20 Identities=40% Similarity=0.586 Sum_probs=15.8
Q ss_pred ccccchhHHHHHHHHhcCCC
Q psy14390 44 ELNLNRPAYLAWLVARLPCK 63 (64)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~~ 63 (64)
+-++++|.|-.-|-|-+-|.
T Consensus 30 e~Nvd~p~Y~~LL~a~l~C~ 49 (56)
T PF01563_consen 30 EDNVDNPGYDDLLEAVLRCP 49 (56)
T ss_dssp HCTSSSTTHHHHHHHHCC--
T ss_pred HHhCCCccHHHHHHHHhhCC
Confidence 44699999999999999884
Done!