Query psy378
Match_columns 107
No_of_seqs 36 out of 38
Neff 2.5
Searched_HMMs 46136
Date Fri Aug 16 17:10:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy378.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/378hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14228 MOR2-PAG1_mid: Cell m 99.3 5.2E-13 1.1E-17 122.8 -0.4 59 26-86 667-737 (1120)
2 KOG1825|consensus 96.3 0.0022 4.7E-08 64.0 2.1 68 26-96 1368-1437(2206)
3 PRK15115 response regulator Gl 62.2 10 0.00022 30.3 3.4 26 45-70 338-364 (444)
4 PF07539 DRIM: Down-regulated 57.5 8.6 0.00019 28.1 2.1 48 54-104 85-133 (141)
5 TIGR01818 ntrC nitrogen regula 56.3 14 0.0003 29.6 3.3 26 45-70 338-364 (463)
6 PF15161 Neuropep_like: Neurop 55.6 5.4 0.00012 27.2 0.7 11 49-59 53-63 (65)
7 PF08542 Rep_fac_C: Replicatio 53.1 25 0.00054 22.2 3.5 44 40-84 4-47 (89)
8 TIGR02915 PEP_resp_reg putativ 51.6 20 0.00043 28.7 3.4 27 44-70 342-369 (445)
9 PRK10365 transcriptional regul 51.5 20 0.00043 28.4 3.4 23 45-67 343-366 (441)
10 PRK11608 pspF phage shock prot 50.3 17 0.00037 29.0 2.9 22 45-66 211-233 (326)
11 PRK10923 glnG nitrogen regulat 48.9 23 0.0005 28.6 3.4 22 45-66 342-364 (469)
12 TIGR02974 phageshock_pspF psp 47.6 20 0.00043 28.9 2.9 23 44-66 203-226 (329)
13 cd08339 DED_DEDD-like Death Ef 44.0 14 0.00031 26.9 1.4 52 30-84 26-83 (97)
14 PRK10820 DNA-binding transcrip 41.7 25 0.00053 30.1 2.7 24 41-64 404-428 (520)
15 TIGR01817 nifA Nif-specific re 41.1 34 0.00074 28.8 3.4 23 45-67 399-422 (534)
16 TIGR03420 DnaA_homol_Hda DnaA 39.9 36 0.00078 24.3 2.9 24 46-69 182-205 (226)
17 PRK11388 DNA-binding transcrip 36.8 41 0.00088 29.0 3.3 24 45-68 525-549 (638)
18 cd00397 DNA_BRE_C DNA breaking 36.1 51 0.0011 21.2 3.0 36 43-79 1-36 (164)
19 PRK05022 anaerobic nitric oxid 35.8 44 0.00096 28.3 3.3 22 44-65 390-412 (509)
20 PRK07308 flavodoxin; Validated 34.5 36 0.00078 23.4 2.2 35 26-61 50-85 (146)
21 PF12833 HTH_18: Helix-turn-he 33.9 1.1E+02 0.0025 18.6 4.3 41 58-98 8-48 (81)
22 PRK15429 formate hydrogenlyase 33.8 51 0.0011 28.9 3.5 21 45-65 580-601 (686)
23 PF03004 Transposase_24: Plant 33.5 26 0.00056 24.1 1.3 13 45-57 2-14 (141)
24 PRK11361 acetoacetate metaboli 32.3 63 0.0014 25.8 3.5 23 45-67 347-370 (457)
25 smart00871 AraC_E_bind Bacteri 32.0 68 0.0015 20.4 3.0 30 31-60 95-125 (158)
26 COG3829 RocR Transcriptional r 30.9 29 0.00063 31.6 1.6 28 35-62 440-468 (560)
27 cd01182 INT_REC_C DNA breaking 29.2 75 0.0016 19.8 2.8 36 43-79 1-36 (162)
28 PF09261 Alpha-mann_mid: Alpha 29.1 39 0.00084 21.7 1.5 17 37-53 40-57 (80)
29 PF05381 Peptidase_C21: Tymovi 28.6 39 0.00084 24.7 1.6 40 36-77 10-49 (104)
30 TIGR02329 propionate_PrpR prop 28.2 60 0.0013 28.4 2.9 24 42-65 418-442 (526)
31 PF00616 RasGAP: GTPase-activa 27.1 38 0.00083 24.0 1.4 50 42-91 104-161 (197)
32 PF01140 Gag_MA: Matrix protei 25.5 1.1E+02 0.0024 23.2 3.6 38 46-83 32-84 (129)
33 PF07194 P2: P2 response regul 23.6 77 0.0017 20.6 2.2 23 27-52 1-23 (84)
34 PF00589 Phage_integrase: Phag 22.7 1.2E+02 0.0026 19.8 3.0 35 42-78 6-41 (173)
35 PF14775 NYD-SP28_assoc: Sperm 21.5 51 0.0011 21.2 1.0 29 35-63 5-33 (60)
36 PF14465 NFRKB_winged: NFRKB W 20.3 32 0.0007 24.7 -0.1 41 41-81 31-71 (100)
37 PF13358 DDE_3: DDE superfamil 20.2 1.3E+02 0.0028 19.2 2.7 27 26-53 106-132 (146)
No 1
>PF14228 MOR2-PAG1_mid: Cell morphogenesis central region
Probab=99.27 E-value=5.2e-13 Score=122.77 Aligned_cols=59 Identities=32% Similarity=0.560 Sum_probs=51.1
Q ss_pred cceeEEEeecCCCcChHHHHHHHHHHHhcCCCchHHHHHHHHHHhC----CC--------cchhhhhhhHHHH
Q psy378 26 NYVNYDKIDPFADELPKEIEDVWATLCSCWPNNMKVIIRYLIIMSG----MA--------PNQLLNYLSMKVI 86 (107)
Q Consensus 26 NNL~~yiTak~~De~p~Eie~lW~TL~~~WPnNLrvILryLiimsg----~s--------p~~LLpy~KrvVI 86 (107)
||| ||||+||||++|.|||++|.+|+.+ |.|+++||+|||..+- -. +.+++|++||+|+
T Consensus 667 ~nL-~~iT~k~~d~~~~Eve~lW~~L~~~-~~N~~~il~FLi~~~le~~~~~~~~~~~~~~~~~~~~~K~v~~ 737 (1120)
T PF14228_consen 667 NNL-FYITIKFGDDHPNEVEALWIALASN-PQNIRVILDFLIELGLERCDQNASKEISVAFATLLPYAKRVVL 737 (1120)
T ss_pred HHH-HHHHHHhccccHHHHHHHHHHHhcC-cccHHHHHHHHHHHhhhhccccchhhhhhhhhhhccccceeeE
Confidence 999 9999999999999999999999986 5899999999997632 21 2379999999875
No 2
>KOG1825|consensus
Probab=96.27 E-value=0.0022 Score=63.95 Aligned_cols=68 Identities=22% Similarity=0.342 Sum_probs=52.4
Q ss_pred cceeEEEeecCCCcChHHHHHHHHHHHh-cCCCchHHHHHHHHHHhCCCcc-hhhhhhhHHHHHHHHHHHhCC
Q psy378 26 NYVNYDKIDPFADELPKEIEDVWATLCS-CWPNNMKVIIRYLIIMSGMAPN-QLLNYLSMKVIIRYLIIMSGM 96 (107)
Q Consensus 26 NNL~~yiTak~~De~p~Eie~lW~TL~~-~WPnNLrvILryLiimsg~sp~-~LLpy~KrvVIi~yl~~~~gm 96 (107)
+++ +|+|.+++|..|-|+|++|.+++. ..--|..+.+-|.+..+-=-++ +++||+||++| ||.=++|-
T Consensus 1368 ~dl-~~vt~~~~~~~p~eie~lW~S~a~t~~~iN~~~yl~~~~~~~~~~~~~~~~~~~k~I~l--YLa~i~~~ 1437 (2206)
T KOG1825|consen 1368 EDL-YYVTIRHEDQLPNEIEKLWSSLALTNRNINPVLYLLITKSIEDCRSNASFVSYAKRISL--YLARICGQ 1437 (2206)
T ss_pred hhh-heehhhccCCCcchHhhcccchhhcccccchhhhhhHhhcCcccccchHHHHHHHHHhh--hhhccccc
Confidence 899 999999999999999999999995 4555666655554444433344 89999999976 67666664
No 3
>PRK15115 response regulator GlrR; Provisional
Probab=62.20 E-value=10 Score=30.26 Aligned_cols=26 Identities=19% Similarity=0.488 Sum_probs=19.3
Q ss_pred HHHHHHHHh-cCCCchHHHHHHHHHHh
Q psy378 45 EDVWATLCS-CWPNNMKVIIRYLIIMS 70 (107)
Q Consensus 45 e~lW~TL~~-~WPnNLrvILryLiims 70 (107)
++++..|.. .||+|+|-..+.+--++
T Consensus 338 ~~a~~~L~~~~WpgNvreL~~~i~~~~ 364 (444)
T PRK15115 338 TDAMKRLMTASWPGNVRQLVNVIEQCV 364 (444)
T ss_pred HHHHHHHHhCCCCChHHHHHHHHHHHH
Confidence 678888887 59999988776664433
No 4
>PF07539 DRIM: Down-regulated in metastasis; InterPro: IPR011430 These eukaryotic proteins include DRIM (Down-Regulated In Metastasis) (O75691 from SWISSPROT), which is differentially expressed in metastatic and non-metastatic human breast carcinoma cells []. It is believed to be involved in processing of non-coding RNA [].
Probab=57.46 E-value=8.6 Score=28.15 Aligned_cols=48 Identities=21% Similarity=0.254 Sum_probs=35.2
Q ss_pred cCCCchHHHHHHHHHHhCCCcchhhh-hhhHHHHHHHHHHHhCCCccccccc
Q psy378 54 CWPNNMKVIIRYLIIMSGMAPNQLLN-YLSMKVIIRYLIIMSGMAPNQLLNY 104 (107)
Q Consensus 54 ~WPnNLrvILryLiimsg~sp~~LLp-y~KrvVIi~yl~~~~gma~~~ll~y 104 (107)
+.|.=+++++|-|+.-.--....--. -.+|..|+||| +|+.+.|+-++
T Consensus 85 hR~~l~pvvlRILygk~~~~~~~~~~~~~rR~aIL~~L---~~l~~~El~~F 133 (141)
T PF07539_consen 85 HRPELMPVVLRILYGKMQSRKGSGSKKASRRAAILRFL---AGLSEEELGLF 133 (141)
T ss_pred HHhHHHHHHHHHHHHHHhhcCCCCCcchHHHHHHHHHH---hCCCHHHHHHH
Confidence 56677899999998766554443333 48999999997 78888877554
No 5
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=56.31 E-value=14 Score=29.60 Aligned_cols=26 Identities=15% Similarity=0.365 Sum_probs=19.1
Q ss_pred HHHHHHHHh-cCCCchHHHHHHHHHHh
Q psy378 45 EDVWATLCS-CWPNNMKVIIRYLIIMS 70 (107)
Q Consensus 45 e~lW~TL~~-~WPnNLrvILryLiims 70 (107)
++++..|.. .||.|+|-+-+.+--++
T Consensus 338 ~~a~~~L~~~~wpgNvreL~~~~~~~~ 364 (463)
T TIGR01818 338 PEALERLKQLRWPGNVRQLENLCRWLT 364 (463)
T ss_pred HHHHHHHHhCCCCChHHHHHHHHHHHH
Confidence 567788886 59999988777664443
No 6
>PF15161 Neuropep_like: Neuropeptide-like
Probab=55.65 E-value=5.4 Score=27.21 Aligned_cols=11 Identities=55% Similarity=1.555 Sum_probs=9.4
Q ss_pred HHHHhcCCCch
Q psy378 49 ATLCSCWPNNM 59 (107)
Q Consensus 49 ~TL~~~WPnNL 59 (107)
.+||+|||.|.
T Consensus 53 RaLc~C~pa~~ 63 (65)
T PF15161_consen 53 RALCDCWPANS 63 (65)
T ss_pred HHHHhcccccc
Confidence 57999999984
No 7
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=53.12 E-value=25 Score=22.24 Aligned_cols=44 Identities=16% Similarity=0.209 Sum_probs=28.0
Q ss_pred ChHHHHHHHHHHHhcCCCchHHHHHHHHHHhCCCcchhhhhhhHH
Q psy378 40 LPKEIEDVWATLCSCWPNNMKVIIRYLIIMSGMAPNQLLNYLSMK 84 (107)
Q Consensus 40 ~p~Eie~lW~TL~~~WPnNLrvILryLiimsg~sp~~LLpy~Krv 84 (107)
+|+++++++.++...==...+..+.=++.. |.++++++...-++
T Consensus 4 ~~~~i~~i~~~~~~~~~~~~~~~~~~l~~~-G~s~~~Il~~l~~~ 47 (89)
T PF08542_consen 4 PPEVIEEILESCLNGDFKEARKKLYELLVE-GYSASDILKQLHEV 47 (89)
T ss_dssp -HHHHHHHHHHHHHTCHHHHHHHHHHHHHT-T--HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhCCHHHHHHHHHHHHHc-CCCHHHHHHHHHHH
Confidence 468999999998775333345555556666 99998777655444
No 8
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=51.57 E-value=20 Score=28.70 Aligned_cols=27 Identities=19% Similarity=0.385 Sum_probs=18.9
Q ss_pred HHHHHHHHHh-cCCCchHHHHHHHHHHh
Q psy378 44 IEDVWATLCS-CWPNNMKVIIRYLIIMS 70 (107)
Q Consensus 44 ie~lW~TL~~-~WPnNLrvILryLiims 70 (107)
-++.+..|.. .||.|+|-.-+.+--.+
T Consensus 342 ~~~a~~~L~~~~wpgNvreL~~~i~~a~ 369 (445)
T TIGR02915 342 TDDALRALEAHAWPGNVRELENKVKRAV 369 (445)
T ss_pred CHHHHHHHHhCCCCChHHHHHHHHHHHH
Confidence 4578888886 59999887665554333
No 9
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=51.49 E-value=20 Score=28.40 Aligned_cols=23 Identities=17% Similarity=0.349 Sum_probs=17.6
Q ss_pred HHHHHHHHh-cCCCchHHHHHHHH
Q psy378 45 EDVWATLCS-CWPNNMKVIIRYLI 67 (107)
Q Consensus 45 e~lW~TL~~-~WPnNLrvILryLi 67 (107)
++++..|+. .||.|+|-..+.+=
T Consensus 343 ~~a~~~L~~~~wpgN~reL~~~~~ 366 (441)
T PRK10365 343 PQAMDLLIHYDWPGNIRELENAVE 366 (441)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHH
Confidence 567788887 59999988766553
No 10
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=50.30 E-value=17 Score=28.97 Aligned_cols=22 Identities=27% Similarity=0.554 Sum_probs=16.5
Q ss_pred HHHHHHHHh-cCCCchHHHHHHH
Q psy378 45 EDVWATLCS-CWPNNMKVIIRYL 66 (107)
Q Consensus 45 e~lW~TL~~-~WPnNLrvILryL 66 (107)
++++..|.. .||.|+|-.-+.+
T Consensus 211 ~~al~~L~~y~WPGNvrEL~~vl 233 (326)
T PRK11608 211 ERARETLLNYRWPGNIRELKNVV 233 (326)
T ss_pred HHHHHHHHhCCCCcHHHHHHHHH
Confidence 578888887 5999988655443
No 11
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=48.88 E-value=23 Score=28.62 Aligned_cols=22 Identities=23% Similarity=0.463 Sum_probs=16.6
Q ss_pred HHHHHHHHh-cCCCchHHHHHHH
Q psy378 45 EDVWATLCS-CWPNNMKVIIRYL 66 (107)
Q Consensus 45 e~lW~TL~~-~WPnNLrvILryL 66 (107)
++++..|.. .||.|+|-.-+.+
T Consensus 342 ~~a~~~L~~~~wpgNv~eL~~~i 364 (469)
T PRK10923 342 PETEAALTRLAWPGNVRQLENTC 364 (469)
T ss_pred HHHHHHHHhCCCCChHHHHHHHH
Confidence 578888887 5999988755443
No 12
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=47.57 E-value=20 Score=28.86 Aligned_cols=23 Identities=17% Similarity=0.433 Sum_probs=17.3
Q ss_pred HHHHHHHHHh-cCCCchHHHHHHH
Q psy378 44 IEDVWATLCS-CWPNNMKVIIRYL 66 (107)
Q Consensus 44 ie~lW~TL~~-~WPnNLrvILryL 66 (107)
=++++..|.. .||.|+|-.-+.+
T Consensus 203 s~~a~~~L~~y~WPGNvrEL~n~i 226 (329)
T TIGR02974 203 TPQAREQLLEYHWPGNVRELKNVV 226 (329)
T ss_pred CHHHHHHHHhCCCCchHHHHHHHH
Confidence 3578888887 5999998765544
No 13
>cd08339 DED_DEDD-like Death Effector Domain of DEDD and DEDD2. Death Effector Domain (DED) found in DEDD and DEDD2. Both proteins have a single N-terminal DED and a long C-terminal portion with no known domains. DEDD has been shown to block mitotic progression by inhibiting Cdk1 and to be involved in regulating the insulin signaling cascade. DEDD and DEDD2 can bind to themselves, to each other, and to the two tandem DED-containing caspases, caspase-8 and -10. In general, DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes.
Probab=44.00 E-value=14 Score=26.88 Aligned_cols=52 Identities=23% Similarity=0.394 Sum_probs=37.4
Q ss_pred EEEeecCCCcCh---HHHHHHHHHHH---hcCCCchHHHHHHHHHHhCCCcchhhhhhhHH
Q psy378 30 YDKIDPFADELP---KEIEDVWATLC---SCWPNNMKVIIRYLIIMSGMAPNQLLNYLSMK 84 (107)
Q Consensus 30 ~yiTak~~De~p---~Eie~lW~TL~---~~WPnNLrvILryLiimsg~sp~~LLpy~Krv 84 (107)
|-++..|+++|| +.=-++--.|- .|=-+|++-+++.|=|++ -.+||||+.++
T Consensus 26 FL~~e~~~~~~~~~~~sG~e~lLeLErrg~cde~N~~~llqLLRilt---RHDLlp~v~~k 83 (97)
T cd08339 26 FLFVDVIDDYERGMIRSGRDFLLALERQGRCDETNFRQVLQLLRIIT---RHDLLPYVTLK 83 (97)
T ss_pred HHHHHhcccccCCCcccHHHHHHHHHHhCCCccccHHHHHHHHHHHH---HhcchHHHHhh
Confidence 344555777887 32334555555 478899999999999886 46999998765
No 14
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=41.74 E-value=25 Score=30.07 Aligned_cols=24 Identities=29% Similarity=0.602 Sum_probs=17.2
Q ss_pred hHHHHHHHHHHHhc-CCCchHHHHH
Q psy378 41 PKEIEDVWATLCSC-WPNNMKVIIR 64 (107)
Q Consensus 41 p~Eie~lW~TL~~~-WPnNLrvILr 64 (107)
|+-=++++..|..+ ||.|+|-.-+
T Consensus 404 ~~ls~~a~~~L~~y~WPGNvreL~n 428 (520)
T PRK10820 404 PKLAADLNTVLTRYGWPGNVRQLKN 428 (520)
T ss_pred CCcCHHHHHHHhcCCCCCHHHHHHH
Confidence 33335778889886 9999998433
No 15
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=41.10 E-value=34 Score=28.83 Aligned_cols=23 Identities=30% Similarity=0.639 Sum_probs=17.0
Q ss_pred HHHHHHHHhc-CCCchHHHHHHHH
Q psy378 45 EDVWATLCSC-WPNNMKVIIRYLI 67 (107)
Q Consensus 45 e~lW~TL~~~-WPnNLrvILryLi 67 (107)
++++..|..+ ||.|+|-.-+.+-
T Consensus 399 ~~a~~~L~~~~WPGNvrEL~~v~~ 422 (534)
T TIGR01817 399 PSAIRVLMSCKWPGNVRELENCLE 422 (534)
T ss_pred HHHHHHHHhCCCCChHHHHHHHHH
Confidence 4677888875 9999987665543
No 16
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=39.92 E-value=36 Score=24.28 Aligned_cols=24 Identities=17% Similarity=0.131 Sum_probs=18.3
Q ss_pred HHHHHHHhcCCCchHHHHHHHHHH
Q psy378 46 DVWATLCSCWPNNMKVIIRYLIIM 69 (107)
Q Consensus 46 ~lW~TL~~~WPnNLrvILryLiim 69 (107)
++...|+..||.|++...+.+=-+
T Consensus 182 ~~l~~L~~~~~gn~r~L~~~l~~~ 205 (226)
T TIGR03420 182 EVADYLLRHGSRDMGSLMALLDAL 205 (226)
T ss_pred HHHHHHHHhccCCHHHHHHHHHHH
Confidence 456778888999999888876443
No 17
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=36.76 E-value=41 Score=28.98 Aligned_cols=24 Identities=29% Similarity=0.379 Sum_probs=16.9
Q ss_pred HHHHHHHHh-cCCCchHHHHHHHHH
Q psy378 45 EDVWATLCS-CWPNNMKVIIRYLII 68 (107)
Q Consensus 45 e~lW~TL~~-~WPnNLrvILryLii 68 (107)
++++..|.. .||.|+|-.-+.+--
T Consensus 525 ~~a~~~L~~y~WPGNvreL~~~l~~ 549 (638)
T PRK11388 525 DDALARLVSYRWPGNDFELRSVIEN 549 (638)
T ss_pred HHHHHHHHcCCCCChHHHHHHHHHH
Confidence 467778876 599998876554433
No 18
>cd00397 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl gener
Probab=36.10 E-value=51 Score=21.16 Aligned_cols=36 Identities=22% Similarity=0.355 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhcCCCchHHHHHHHHHHhCCCcchhhh
Q psy378 43 EIEDVWATLCSCWPNNMKVIIRYLIIMSGMAPNQLLN 79 (107)
Q Consensus 43 Eie~lW~TL~~~WPnNLrvILryLiimsg~sp~~LLp 79 (107)
|++.+|..+-...+.-.+.++.+++ -+|+-+.++.-
T Consensus 1 e~~~l~~~~~~~~~~~~~~~~~l~~-~tG~R~~Ei~~ 36 (164)
T cd00397 1 EIERLLAAAEASTPERLYLALLLLL-ATGLRISELCA 36 (164)
T ss_pred CHHHHHHHhhhccccHHHHHHHHHH-HhCCCHHHHhC
Confidence 5788888777653333444444443 36888876643
No 19
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=35.78 E-value=44 Score=28.27 Aligned_cols=22 Identities=23% Similarity=0.398 Sum_probs=16.4
Q ss_pred HHHHHHHHHh-cCCCchHHHHHH
Q psy378 44 IEDVWATLCS-CWPNNMKVIIRY 65 (107)
Q Consensus 44 ie~lW~TL~~-~WPnNLrvILry 65 (107)
=++++..|.. .||.|+|-.-+.
T Consensus 390 s~~a~~~L~~y~WPGNvrEL~~~ 412 (509)
T PRK05022 390 SPAAQAALLAYDWPGNVRELEHV 412 (509)
T ss_pred CHHHHHHHHhCCCCCcHHHHHHH
Confidence 3577888887 599998865553
No 20
>PRK07308 flavodoxin; Validated
Probab=34.48 E-value=36 Score=23.45 Aligned_cols=35 Identities=20% Similarity=0.221 Sum_probs=28.4
Q ss_pred cceeEEEeecCC-CcChHHHHHHHHHHHhcCCCchHH
Q psy378 26 NYVNYDKIDPFA-DELPKEIEDVWATLCSCWPNNMKV 61 (107)
Q Consensus 26 NNL~~yiTak~~-De~p~Eie~lW~TL~~~WPnNLrv 61 (107)
.-+ ...+.+|| .++|+++++++..|...+..|.++
T Consensus 50 d~v-i~g~~t~g~G~~p~~~~~fl~~l~~~~l~~k~~ 85 (146)
T PRK07308 50 DIA-IVATYTYGDGELPDEIVDFYEDLADLDLSGKIY 85 (146)
T ss_pred CEE-EEEeCccCCCCCCHHHHHHHHHHhcCCCCCCEE
Confidence 456 77899998 558889999999999888777654
No 21
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=33.87 E-value=1.1e+02 Score=18.62 Aligned_cols=41 Identities=17% Similarity=0.165 Sum_probs=28.0
Q ss_pred chHHHHHHHHHHhCCCcchhhhhhhHHHHHHHHHHHhCCCc
Q psy378 58 NMKVIIRYLIIMSGMAPNQLLNYLSMKVIIRYLIIMSGMAP 98 (107)
Q Consensus 58 NLrvILryLiimsg~sp~~LLpy~KrvVIi~yl~~~~gma~ 98 (107)
+-+-+-+.+--.+|+++.+++...|...+.+.|+--.+++-
T Consensus 8 s~~~l~~~f~~~~g~s~~~~~~~~R~~~a~~~L~~~~~~~i 48 (81)
T PF12833_consen 8 SERYLSRIFKKETGMSFKQYLRELRLQRAKELLRQNTDLSI 48 (81)
T ss_dssp -HHHHHHHHHHHHSS-HHHHHHHHHHHHHHHHHHHHTT--H
T ss_pred CHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHhhcccH
Confidence 34455666777799999999999999988888865444443
No 22
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=33.82 E-value=51 Score=28.86 Aligned_cols=21 Identities=24% Similarity=0.534 Sum_probs=15.6
Q ss_pred HHHHHHHHh-cCCCchHHHHHH
Q psy378 45 EDVWATLCS-CWPNNMKVIIRY 65 (107)
Q Consensus 45 e~lW~TL~~-~WPnNLrvILry 65 (107)
++++..|.. .||.|+|-.-+.
T Consensus 580 ~~al~~L~~y~WPGNvrEL~~~ 601 (686)
T PRK15429 580 AETLRTLSNMEWPGNVRELENV 601 (686)
T ss_pred HHHHHHHHhCCCCCcHHHHHHH
Confidence 478888886 599998755443
No 23
>PF03004 Transposase_24: Plant transposase (Ptta/En/Spm family); InterPro: IPR004252 Transposase proteins are necessary for efficient DNA transposition. This family includes various plant transposases from the Ptta and En/Spm families []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=33.47 E-value=26 Score=24.11 Aligned_cols=13 Identities=23% Similarity=0.777 Sum_probs=11.2
Q ss_pred HHHHHHHHhcCCC
Q psy378 45 EDVWATLCSCWPN 57 (107)
Q Consensus 45 e~lW~TL~~~WPn 57 (107)
++.|..||.+|.+
T Consensus 2 ~~~W~~lv~~w~s 14 (141)
T PF03004_consen 2 PEQWNWLVEYWSS 14 (141)
T ss_pred HHHHHHHHHHhCC
Confidence 5789999999974
No 24
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=32.29 E-value=63 Score=25.81 Aligned_cols=23 Identities=17% Similarity=0.432 Sum_probs=16.2
Q ss_pred HHHHHHHHh-cCCCchHHHHHHHH
Q psy378 45 EDVWATLCS-CWPNNMKVIIRYLI 67 (107)
Q Consensus 45 e~lW~TL~~-~WPnNLrvILryLi 67 (107)
+++...|.. .||.|++-.-+.+-
T Consensus 347 ~~a~~~L~~~~wpgNv~eL~~~~~ 370 (457)
T PRK11361 347 PMAMSLLTAWSWPGNIRELSNVIE 370 (457)
T ss_pred HHHHHHHHcCCCCCcHHHHHHHHH
Confidence 456667776 59999987666553
No 25
>smart00871 AraC_E_bind Bacterial transcription activator, effector binding domain. This domain is found in the probable effector binding domain of a number of different bacterial transcription activators PUBMED:10802742 and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.
Probab=31.99 E-value=68 Score=20.37 Aligned_cols=30 Identities=20% Similarity=0.412 Sum_probs=22.8
Q ss_pred EEeecCCCcChHHHHHHHHHHHhcC-CCchH
Q psy378 31 DKIDPFADELPKEIEDVWATLCSCW-PNNMK 60 (107)
Q Consensus 31 yiTak~~De~p~Eie~lW~TL~~~W-PnNLr 60 (107)
|+++++....++++.+.|..|...| ++++.
T Consensus 95 y~~~~~~g~~~~~~~~~~~~l~~~~~~~~~~ 125 (158)
T smart00871 95 YAVFTHKGGSYDEIQETWEAIYGEWLPNSGY 125 (158)
T ss_pred EEEEEEcCCCHHHHHHHHHHHHHhhcccCCC
Confidence 6777776546788999999999876 55544
No 26
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=30.94 E-value=29 Score=31.57 Aligned_cols=28 Identities=21% Similarity=0.459 Sum_probs=20.5
Q ss_pred cCCCcChHHHHHHHHHHHhc-CCCchHHH
Q psy378 35 PFADELPKEIEDVWATLCSC-WPNNMKVI 62 (107)
Q Consensus 35 k~~De~p~Eie~lW~TL~~~-WPnNLrvI 62 (107)
+|+-+++.--+++|..|-++ ||.|.|-+
T Consensus 440 ~~~~~v~~ls~~a~~~L~~y~WPGNVREL 468 (560)
T COG3829 440 RYGRNVKGLSPDALALLLRYDWPGNVREL 468 (560)
T ss_pred HcCCCcccCCHHHHHHHHhCCCCchHHHH
Confidence 45555554456899999986 99998854
No 27
>cd01182 INT_REC_C DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family include the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many intergrase/recombinases also have N-terminal domains, which show little sequence or structure similarity.
Probab=29.23 E-value=75 Score=19.82 Aligned_cols=36 Identities=22% Similarity=0.338 Sum_probs=19.0
Q ss_pred HHHHHHHHHHhcCCCchHHHHHHHHHHhCCCcchhhh
Q psy378 43 EIEDVWATLCSCWPNNMKVIIRYLIIMSGMAPNQLLN 79 (107)
Q Consensus 43 Eie~lW~TL~~~WPnNLrvILryLiimsg~sp~~LLp 79 (107)
|++.+|.+.....+.=.+.++..++ .+|+-|.++..
T Consensus 1 ~~~~l~~~~~~~~~~~~~~~~~l~~-~~G~R~~ei~~ 36 (162)
T cd01182 1 ELKKLLAALKKDTAPRDRALILLLL-YTGLRVSELLA 36 (162)
T ss_pred CHHHHHHHhcccccHHHHHHHHHHH-HhCCCHHHHhh
Confidence 4677777766542222333333333 37777776543
No 28
>PF09261 Alpha-mann_mid: Alpha mannosidase, middle domain; InterPro: IPR015341 Members of this entry belong to the glycosyl hydrolase family 38, This domain, which is found in the central region adopts a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. The domain is predominantly found in the enzyme alpha-mannosidase []. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0008270 zinc ion binding; PDB: 1O7D_C 3LVT_A 3CZN_A 2FYV_A 3D50_A 3EJU_A 3EJS_A 3DX3_A 3BVX_A 3BUQ_A ....
Probab=29.08 E-value=39 Score=21.72 Aligned_cols=17 Identities=29% Similarity=0.735 Sum_probs=13.0
Q ss_pred CCcCh-HHHHHHHHHHHh
Q psy378 37 ADELP-KEIEDVWATLCS 53 (107)
Q Consensus 37 ~De~p-~Eie~lW~TL~~ 53 (107)
+++.| ++++++|.+|.-
T Consensus 40 ~~~~~~~~l~~~w~~l~~ 57 (80)
T PF09261_consen 40 GGDYPQEELEKAWKALLL 57 (80)
T ss_dssp HSG-HHHHHHHHHHHHHC
T ss_pred CccccHHHHHHHHHHHHH
Confidence 44566 899999999884
No 29
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=28.62 E-value=39 Score=24.66 Aligned_cols=40 Identities=25% Similarity=0.459 Sum_probs=25.2
Q ss_pred CCCcChHHHHHHHHHHHhcCCCchHHHHHHHHHHhCCCcchh
Q psy378 36 FADELPKEIEDVWATLCSCWPNNMKVIIRYLIIMSGMAPNQL 77 (107)
Q Consensus 36 ~~De~p~Eie~lW~TL~~~WPnNLrvILryLiimsg~sp~~L 77 (107)
+++.-.-..|++|.+||.--|.-|= -+=-|.--|+|.|-|
T Consensus 10 ~s~at~~~~~~LW~~L~~~lPDSlL--~n~ei~~~GLSTDhl 49 (104)
T PF05381_consen 10 ISQATSISPETLWATLCEILPDSLL--DNPEIRTLGLSTDHL 49 (104)
T ss_pred hhhhhCCCHHHHHHHHHHhCchhhc--CchhhhhcCCcHHHH
Confidence 3444443468999999998887542 222345567777743
No 30
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=28.24 E-value=60 Score=28.38 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHh-cCCCchHHHHHH
Q psy378 42 KEIEDVWATLCS-CWPNNMKVIIRY 65 (107)
Q Consensus 42 ~Eie~lW~TL~~-~WPnNLrvILry 65 (107)
+.+++++..|.. .||.|+|-.-+.
T Consensus 418 ~~~~~~~~~L~~y~WPGNvrEL~nv 442 (526)
T TIGR02329 418 QVLAGVADPLQRYPWPGNVRELRNL 442 (526)
T ss_pred HHhHHHHHHHHhCCCCchHHHHHHH
Confidence 335566777887 599998765443
No 31
>PF00616 RasGAP: GTPase-activator protein for Ras-like GTPase; InterPro: IPR001936 Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP []. This intrinsic GTPase activity of ras is stimulated by a family of proteins collectively known as 'GAP' or GTPase-activating proteins [, ]. As it is the GTP bound form of ras which is active, these proteins are said to be down-regulators of ras. The Ras GTPase-activating proteins are quite large (from 765 residues for sar1 to 3079 residues for IRA2) but share only a limited (about 250 residues) region of sequence similarity, referred to as the 'catalytic domain' or rasGAP domain. Note: There are distinctly different GAPs for the rap and rho/rac subfamilies of ras-like proteins (reviewed in reference []) that do not share sequence similarity with ras GAPs.; GO: 0005096 GTPase activator activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3BXJ_B 1WQ1_G 1WER_A 1NF1_A 3FAY_A.
Probab=27.14 E-value=38 Score=24.01 Aligned_cols=50 Identities=14% Similarity=0.277 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHh---cCCCchHHHHHHHHHHhCCC-----cchhhhhhhHHHHHHHHH
Q psy378 42 KEIEDVWATLCS---CWPNNMKVIIRYLIIMSGMA-----PNQLLNYLSMKVIIRYLI 91 (107)
Q Consensus 42 ~Eie~lW~TL~~---~WPnNLrvILryLiimsg~s-----p~~LLpy~KrvVIi~yl~ 91 (107)
+-.+.+|.++.+ ++|.-+|.+.+.+.....-. +++....+...+.+||+.
T Consensus 104 ~~~~~~~~~i~~s~~~~P~~lr~i~~~i~~~~~~~fp~~~~~~~~~~v~~fiflrfi~ 161 (197)
T PF00616_consen 104 ELCESFLDAIISSIDQIPPSLRYICKQIYEAVEKKFPDASPEEILSAVGGFIFLRFIC 161 (197)
T ss_dssp HHHHHHHHHHHGGGGGS-HHHHHHHHHHHHHHHHHTTTSSHCHHHHHHHHHHTTTTHH
T ss_pred HHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHHH
Confidence 446778888886 47999999999988876533 357777777788888764
No 32
>PF01140 Gag_MA: Matrix protein (MA), p15; InterPro: IPR000840 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from gamma-retroviruses, such as Moloney murine leukemia virus (MoMLV), Feline leukemia virus (FLV), and Feline sarcoma virus (FESV) [, ]. This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1MN8_B.
Probab=25.48 E-value=1.1e+02 Score=23.19 Aligned_cols=38 Identities=29% Similarity=0.732 Sum_probs=26.9
Q ss_pred HHHHHHHhc-CCC-----------chHHHHHHHHHHhCCCcc---hhhhhhhH
Q psy378 46 DVWATLCSC-WPN-----------NMKVIIRYLIIMSGMAPN---QLLNYLSM 83 (107)
Q Consensus 46 ~lW~TL~~~-WPn-----------NLrvILryLiimsg~sp~---~LLpy~Kr 83 (107)
.=|.|||++ ||. |+.+|++-=-++.+=.|+ +=.||+-.
T Consensus 32 ~kw~tfC~~EWPtf~vGWP~eGTfnl~iI~qVk~~vf~~~p~GhpDQvPYI~t 84 (129)
T PF01140_consen 32 GKWQTFCSSEWPTFGVGWPPEGTFNLSIILQVKRIVFQPGPHGHPDQVPYIVT 84 (129)
T ss_dssp HHHHHHHHTTGGGGSSS--TT----HHHHHHHHHHHTSSCCCS-GGGHHHHHH
T ss_pred cceeeEeeeeccccccCCCCCCccCHHHHHHHHHHHhcCCCCCCCccchHHHH
Confidence 469999974 775 899999988777776642 55677643
No 33
>PF07194 P2: P2 response regulator binding domain; InterPro: IPR010808 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. The response regulators for CheA bind to the P2 domain, which is found between IPR008207 from INTERPRO and IPR004105 from INTERPRO as either one or two copies. Highly flexible linkers connect P2 to the rest of CheA and impart remarkable mobility to the P2 domain. This feature is thought to enhance the inter CheA dimer phosphotransfer reactions within the signalling complex, thereby amplifying the phosphorylation signal [].; GO: 0000155 two-component sensor activity, 0004673 protein histidine kinase activity, 0000160 two-component signal transduction system (phosphorelay), 0006928 cellular component movement; PDB: 1U0S_A.
Probab=23.55 E-value=77 Score=20.63 Aligned_cols=23 Identities=26% Similarity=0.447 Sum_probs=14.4
Q ss_pred ceeEEEeecCCCcChHHHHHHHHHHH
Q psy378 27 YVNYDKIDPFADELPKEIEDVWATLC 52 (107)
Q Consensus 27 NL~~yiTak~~De~p~Eie~lW~TL~ 52 (107)
|. |+++++|.++.+ |+++.+-++
T Consensus 1 k~-y~i~v~~~~~c~--Mk~vRa~~v 23 (84)
T PF07194_consen 1 KV-YHIKVEFDEDCP--MKNVRAFMV 23 (84)
T ss_dssp EE-EEEEEE--TT-S--SHHHHHHHH
T ss_pred CE-EEEEEEECCCCC--chhccHHHH
Confidence 56 899999998887 456666554
No 34
>PF00589 Phage_integrase: Phage integrase family; InterPro: IPR002104 Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The catalytic site residues in CRE recombinase (P06956 from SWISSPROT) are Arg-173, His-289, Arg-292 and Tyr-324.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration; PDB: 1A0P_A 1Z1G_B 1Z19_A 1AE9_A 1Z1B_A 1P7D_B 2A3V_C 1Q3V_E 1Q3U_A 1OUQ_F ....
Probab=22.70 E-value=1.2e+02 Score=19.78 Aligned_cols=35 Identities=23% Similarity=0.455 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHhcCCCchHHHHHH-HHHHhCCCcchhh
Q psy378 42 KEIEDVWATLCSCWPNNMKVIIRY-LIIMSGMAPNQLL 78 (107)
Q Consensus 42 ~Eie~lW~TL~~~WPnNLrvILry-Liimsg~sp~~LL 78 (107)
+|++.+|..+.. +.+.+.-+-+ +...||+-+.+++
T Consensus 6 ~e~~~l~~~~~~--~~~~~~~~~~~l~~~tG~R~~El~ 41 (173)
T PF00589_consen 6 EEIKQLLDALEE--KIPLRNRLIILLLLYTGLRPSELL 41 (173)
T ss_dssp HHHHHHHHHCCT--CSHHHHHHHHHHHHHHT--HHHHH
T ss_pred HHHHHHHHHhhh--cCCHHHHHHHHHHHHHccchhhhh
Confidence 678888888777 4444433222 3345677776554
No 35
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=21.48 E-value=51 Score=21.24 Aligned_cols=29 Identities=24% Similarity=0.440 Sum_probs=21.6
Q ss_pred cCCCcChHHHHHHHHHHHhcCCCchHHHH
Q psy378 35 PFADELPKEIEDVWATLCSCWPNNMKVII 63 (107)
Q Consensus 35 k~~De~p~Eie~lW~TL~~~WPnNLrvIL 63 (107)
++++-.|++-..+|.+|-..|-.=.+|.+
T Consensus 5 ~~~~vip~~~~~~W~~L~~~l~rY~~vL~ 33 (60)
T PF14775_consen 5 RLANVIPDEKIRLWDALENFLKRYNKVLL 33 (60)
T ss_pred HHhhcCChHHHHHHHHHHHHHHHHHHHHH
Confidence 46777899999999999987754444433
No 36
>PF14465 NFRKB_winged: NFRKB Winged Helix-like; PDB: 3U21_B.
Probab=20.31 E-value=32 Score=24.75 Aligned_cols=41 Identities=22% Similarity=0.494 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHhcCCCchHHHHHHHHHHhCCCcchhhhhh
Q psy378 41 PKEIEDVWATLCSCWPNNMKVIIRYLIIMSGMAPNQLLNYL 81 (107)
Q Consensus 41 p~Eie~lW~TL~~~WPnNLrvILryLiimsg~sp~~LLpy~ 81 (107)
|..--+-|-+++.+|+.=+.-.|+||.--++-.|.+.-||+
T Consensus 31 p~s~ln~W~s~~pdWs~Lv~sAL~fLaG~~~~~p~~f~P~V 71 (100)
T PF14465_consen 31 PASPLNDWFSLQPDWSELVQSALQFLAGESGDLPSEFVPYV 71 (100)
T ss_dssp GGGGGSTTGGG-S-CGGGHHHHHHHHTT-SS-S-TT---SE
T ss_pred ccccccchhhcCCCHHHHHHHHHHHhcCCCCCCCCCceeee
Confidence 33344568889999999999999999888888888888887
No 37
>PF13358 DDE_3: DDE superfamily endonuclease
Probab=20.15 E-value=1.3e+02 Score=19.17 Aligned_cols=27 Identities=26% Similarity=0.500 Sum_probs=18.7
Q ss_pred cceeEEEeecCCCcChHHHHHHHHHHHh
Q psy378 26 NYVNYDKIDPFADELPKEIEDVWATLCS 53 (107)
Q Consensus 26 NNL~~yiTak~~De~p~Eie~lW~TL~~ 53 (107)
+++.+.-+-.|+-|+=+ ||++|..|-.
T Consensus 106 ~~~~~~~~P~~sPdLNp-iE~~w~~lk~ 132 (146)
T PF13358_consen 106 RGIELLFLPPYSPDLNP-IENVWGYLKR 132 (146)
T ss_pred cccccccccCcCCccCH-HHHHHHHHHH
Confidence 33434445678877776 9999998864
Done!