Query psy678
Match_columns 60
No_of_seqs 97 out of 99
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 18:12:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy678.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/678hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3689|consensus 98.5 1.2E-07 2.5E-12 73.6 3.6 56 4-59 157-212 (707)
2 PF01590 GAF: GAF domain; Int 96.7 0.0016 3.4E-08 38.5 2.8 31 29-59 1-31 (154)
3 PF13492 GAF_3: GAF domain; PD 96.3 0.0042 9E-08 35.7 2.6 31 29-59 1-31 (129)
4 TIGR01817 nifA Nif-specific re 96.2 0.0087 1.9E-07 44.2 4.5 46 13-59 4-49 (534)
5 PRK15429 formate hydrogenlyase 95.5 0.046 1E-06 41.7 5.9 45 14-59 185-229 (686)
6 PRK11061 fused phosphoenolpyru 94.8 0.047 1E-06 42.7 4.1 44 15-59 4-47 (748)
7 smart00065 GAF Domain present 94.3 0.053 1.2E-06 29.9 2.6 29 29-57 1-29 (149)
8 PF13185 GAF_2: GAF domain; PD 92.3 0.17 3.8E-06 29.4 2.8 31 29-59 3-33 (148)
9 PRK15429 formate hydrogenlyase 92.0 0.29 6.4E-06 37.4 4.4 46 13-59 8-53 (686)
10 COG2203 FhlA FOG: GAF domain [ 91.3 0.65 1.4E-05 26.4 4.4 44 14-58 4-47 (175)
11 PRK05022 anaerobic nitric oxid 85.2 1.6 3.4E-05 32.5 4.1 43 14-57 4-46 (509)
12 PRK10490 sensor protein KdpD; 77.5 11 0.00023 30.2 6.4 54 3-58 502-555 (895)
13 COG2205 KdpD Osmosensitive K+ 76.5 12 0.00025 30.8 6.4 55 2-58 498-552 (890)
14 PF11849 DUF3369: Domain of un 58.5 46 0.00099 21.3 6.0 49 5-54 11-61 (174)
15 KOG3689|consensus 52.3 3.8 8.3E-05 32.7 -0.5 26 30-55 7-32 (707)
16 smart00250 PLEC Plectin repeat 51.6 7.1 0.00015 19.3 0.6 17 43-59 2-18 (38)
17 PF04406 TP6A_N: Type IIB DNA 46.0 19 0.00041 19.9 1.8 30 22-55 39-68 (68)
18 PRK13837 two-component VirA-li 39.9 1.3E+02 0.0028 23.6 6.1 45 14-58 277-322 (828)
19 COG2406 Protein distantly rela 39.3 12 0.00025 25.2 0.3 17 36-52 104-120 (172)
20 COG2893 ManX Phosphotransferas 39.0 76 0.0016 20.3 4.1 46 13-58 13-69 (143)
21 COG3604 FhlA Transcriptional r 36.4 71 0.0015 25.1 4.2 44 15-59 35-78 (550)
22 KOG0479|consensus 33.7 26 0.00056 28.5 1.5 29 24-53 407-445 (818)
23 PF06635 NolV: Nodulation prot 27.7 2.1E+02 0.0046 19.8 5.7 45 3-48 86-130 (207)
24 PF08468 MTS_N: Methyltransfer 26.7 15 0.00032 23.6 -0.7 29 26-55 110-138 (155)
25 COG5211 SSU72 RNA polymerase I 26.4 1.5E+02 0.0033 20.2 4.0 30 14-43 154-183 (197)
26 PF10482 CtIP_N: Tumour-suppre 24.7 64 0.0014 20.6 1.9 6 47-52 70-75 (120)
27 TIGR02916 PEP_his_kin putative 23.7 1.2E+02 0.0026 23.1 3.5 42 16-58 307-348 (679)
28 PF03523 Macscav_rec: Macropha 23.0 1.1E+02 0.0025 16.6 2.4 23 2-24 22-44 (49)
29 PF08256 Antimicrobial20: Aure 22.3 74 0.0016 12.9 1.2 10 16-25 2-11 (13)
30 PF02283 CobU: Cobinamide kina 22.2 2E+02 0.0043 18.5 3.9 41 16-57 82-122 (167)
31 PF04793 Herpes_BBRF1: BRRF1-l 21.9 2.2E+02 0.0047 20.5 4.3 35 10-44 32-66 (284)
32 COG4251 Bacteriophytochrome (l 21.4 2.1E+02 0.0045 23.5 4.5 44 16-59 134-177 (750)
33 PF00681 Plectin: Plectin repe 21.2 41 0.00089 17.1 0.4 17 43-59 2-18 (45)
34 KOG4422|consensus 20.5 82 0.0018 24.9 2.1 34 18-51 194-227 (625)
No 1
>KOG3689|consensus
Probab=98.48 E-value=1.2e-07 Score=73.60 Aligned_cols=56 Identities=36% Similarity=0.536 Sum_probs=53.3
Q ss_pred HHhHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccCCC
Q psy678 4 AQSLLKCENAAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDESS 59 (60)
Q Consensus 4 ~~~~~e~~rnq~LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~~~ 59 (60)
+.++.|.+|+++|+|+++.+|+++.+++.++++++.+++++++|+||+++++|++.
T Consensus 157 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~si~~~~~~~ 212 (707)
T KOG3689|consen 157 ASSRIERKRNQVLLDLADLMFEEQTDRESIFPKILYTARSLLQCTRCSIQLLDMST 212 (707)
T ss_pred HHhhhHHHHHHHHhhhhhHHHHHhcchhcccchhhhhhhhhhhhcccceeeecccc
Confidence 46789999999999999999999999999999999999999999999999999865
No 2
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=96.74 E-value=0.0016 Score=38.55 Aligned_cols=31 Identities=19% Similarity=0.548 Sum_probs=28.6
Q ss_pred cHHHHHHHHHHHHHhhhccchhheeeccCCC
Q psy678 29 SIEQVVVKIMQRAQSLLKCENAAVLLIDESS 59 (60)
Q Consensus 29 sid~li~~im~~a~~Ll~aeRcslflvD~~~ 59 (60)
|++.++.+++..+..+++++||+++++|.+.
T Consensus 1 Dl~~~l~~~~~~l~~~l~~~~~~i~~~d~~~ 31 (154)
T PF01590_consen 1 DLDELLQRILRELAELLGADRASIFLLDPDG 31 (154)
T ss_dssp SHHHHHHHHHHHHHHHHTESEEEEEEEETTT
T ss_pred CHHHHHHHHHHHHHHHHCCCEEEEEEEecCC
Confidence 5899999999999999999999999998764
No 3
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=96.30 E-value=0.0042 Score=35.65 Aligned_cols=31 Identities=26% Similarity=0.580 Sum_probs=27.0
Q ss_pred cHHHHHHHHHHHHHhhhccchhheeeccCCC
Q psy678 29 SIEQVVVKIMQRAQSLLKCENAAVLLIDESS 59 (60)
Q Consensus 29 sid~li~~im~~a~~Ll~aeRcslflvD~~~ 59 (60)
|++.+++.++..+..++++++|.||++|++.
T Consensus 1 dl~~l~~~i~~~l~~~~~~~~~~l~~~d~~~ 31 (129)
T PF13492_consen 1 DLDELLERILELLRELLGADRAALFLLDEDG 31 (129)
T ss_dssp -HHHHHHHHHHHHHHHST-SEEEEEEEETTC
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCC
Confidence 5899999999999999999999999999753
No 4
>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=96.21 E-value=0.0087 Score=44.24 Aligned_cols=46 Identities=17% Similarity=0.229 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccCCC
Q psy678 13 AAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDESS 59 (60)
Q Consensus 13 nq~LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~~~ 59 (60)
-..|.++++.+..+.+ ++.++..|+..+..+++|++|+++++|.++
T Consensus 4 L~~L~~is~~l~~~~d-l~~lL~~il~~l~~~l~a~~~~I~L~d~~~ 49 (534)
T TIGR01817 4 LAALYEISKILSAPTR-LEKTLANVLNVLSNDLGMRHGLITLSDSEG 49 (534)
T ss_pred HHHHHHHHHHHhccCC-HHHHHHHHHHHHHHhcCCCEEEEEEECCCC
Confidence 4578889999988766 999999999999999999999999998764
No 5
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=95.51 E-value=0.046 Score=41.70 Aligned_cols=45 Identities=7% Similarity=0.275 Sum_probs=40.9
Q ss_pred HHHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccCCC
Q psy678 14 AKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDESS 59 (60)
Q Consensus 14 q~LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~~~ 59 (60)
+.|.++++.+-... +++.++..|+..+..+++|++|++++.|.+.
T Consensus 185 ~~L~eIs~~l~s~~-dl~ell~~I~~~i~~~~~a~~~~I~L~d~~~ 229 (686)
T PRK15429 185 RILVAITNAVLSRL-DMDELVSEVAKEIHYYFDIDAISIVLRSHRK 229 (686)
T ss_pred HHHHHHHHHHccCC-CHHHHHHHHHHHHHHHhCCCEEEEEEEECCC
Confidence 78899999998866 5999999999999999999999999998753
No 6
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=94.75 E-value=0.047 Score=42.74 Aligned_cols=44 Identities=16% Similarity=0.264 Sum_probs=38.3
Q ss_pred HHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccCCC
Q psy678 15 KLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDESS 59 (60)
Q Consensus 15 ~LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~~~ 59 (60)
.|.++++.+..... ++.++..|+..+..+++|++|+|+++|.+.
T Consensus 4 ~L~eIs~~L~s~~d-L~e~L~~Iv~~~~~~l~~d~~sI~L~D~~~ 47 (748)
T PRK11061 4 RLREIVEKVASAPR-LNEALDILVTETCLAMDTEVCSVYLADHDR 47 (748)
T ss_pred HHHHHHHHHhccCC-HHHHHHHHHHHHHHHhCCCEEEEEEEECCC
Confidence 36678888877665 999999999999999999999999999754
No 7
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=94.27 E-value=0.053 Score=29.86 Aligned_cols=29 Identities=24% Similarity=0.552 Sum_probs=26.8
Q ss_pred cHHHHHHHHHHHHHhhhccchhheeeccC
Q psy678 29 SIEQVVVKIMQRAQSLLKCENAAVLLIDE 57 (60)
Q Consensus 29 sid~li~~im~~a~~Ll~aeRcslflvD~ 57 (60)
+++.++.+++..+...+++++|.++++|.
T Consensus 1 ~~~~~~~~~~~~l~~~~~~~~~~i~~~~~ 29 (149)
T smart00065 1 DLEELLQTILEELRQLLGADRVLIYLVDE 29 (149)
T ss_pred CHHHHHHHHHHHHHHHhCCceEEEEEEec
Confidence 46788999999999999999999999997
No 8
>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A ....
Probab=92.29 E-value=0.17 Score=29.42 Aligned_cols=31 Identities=19% Similarity=0.384 Sum_probs=27.2
Q ss_pred cHHHHHHHHHHHHHhhhccchhheeeccCCC
Q psy678 29 SIEQVVVKIMQRAQSLLKCENAAVLLIDESS 59 (60)
Q Consensus 29 sid~li~~im~~a~~Ll~aeRcslflvD~~~ 59 (60)
+++.++..++..+..+++|+.+.++++|.++
T Consensus 3 ~~~ell~~~~~~~~~~~~~~~~~i~l~d~~~ 33 (148)
T PF13185_consen 3 DLEELLQQILDALLELTGADAGAIYLYDPDG 33 (148)
T ss_dssp HHHHHHHHHHHHHHHHHS-SEEEEEEEETTS
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCC
Confidence 5899999999999999999999999998763
No 9
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=92.02 E-value=0.29 Score=37.40 Aligned_cols=46 Identities=17% Similarity=0.319 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccCCC
Q psy678 13 AAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDESS 59 (60)
Q Consensus 13 nq~LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~~~ 59 (60)
.+.|+++++.+.. +.+++.++..++...+.++.||++.+.|.|..+
T Consensus 8 ~~~l~~is~~~~~-~~~~~~l~~~l~~~~~~~~~ad~~~i~l~d~~~ 53 (686)
T PRK15429 8 QQGLFDITRTLLQ-QPDLASLCEALSQLVKRSALADNAAIVLWQAQT 53 (686)
T ss_pred HHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhhcccceEEEEEEcCCC
Confidence 4679999888877 556999999999999999999999999999754
No 10
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=91.29 E-value=0.65 Score=26.45 Aligned_cols=44 Identities=20% Similarity=0.377 Sum_probs=36.8
Q ss_pred HHHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccCC
Q psy678 14 AKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDES 58 (60)
Q Consensus 14 q~LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~~ 58 (60)
..+.++++.+..... .+.++..++..+...++++||.++.++.+
T Consensus 4 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 47 (175)
T COG2203 4 ALLNELAAKIAQDLD-LEEILQAALELLAELLGADRGLIYLLDED 47 (175)
T ss_pred HHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHhhccHHhhheeccc
Confidence 345566666666665 99999999999999999999999999875
No 11
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=85.24 E-value=1.6 Score=32.46 Aligned_cols=43 Identities=21% Similarity=0.393 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccC
Q psy678 14 AKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDE 57 (60)
Q Consensus 14 q~LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~ 57 (60)
..|.++++.|-...+ ++..+..++..+...+.|+.|+|++.|.
T Consensus 4 ~~l~eis~~L~~s~d-~~e~L~~vl~~l~~~l~~~~~~l~l~~~ 46 (509)
T PRK05022 4 DALLPIALDLSRGLP-HQDRFQRLLTTLRQVLPCDASALLRLDG 46 (509)
T ss_pred HHHHHHHHHHhcCCC-HHHHHHHHHHHHHHHcCCCEEEEEecCC
Confidence 357889999988885 9999999999999999999999999875
No 12
>PRK10490 sensor protein KdpD; Provisional
Probab=77.54 E-value=11 Score=30.17 Aligned_cols=54 Identities=15% Similarity=0.161 Sum_probs=43.2
Q ss_pred hHHhHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccCC
Q psy678 3 RAQSLLKCENAAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDES 58 (60)
Q Consensus 3 ~~~~~~e~~rnq~LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~~ 58 (60)
.+......++.+.|.++++.+....+ .+.++......+..++++. |.+|+.|..
T Consensus 502 a~~a~~re~~~~~L~els~~L~~a~~-~~~i~~~~~~~l~~~~~~~-~~l~l~~~~ 555 (895)
T PRK10490 502 ARVARYREQRTRHLYEMSKALAVGLS-PEDIAATSEHFLASTFQAR-SQLLLPDDN 555 (895)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCC-HHHHHHHHHHHHHHhhCCC-EEEEEEcCC
Confidence 34455566778899999999987666 8999999999999999984 678887743
No 13
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=76.50 E-value=12 Score=30.82 Aligned_cols=55 Identities=24% Similarity=0.259 Sum_probs=47.5
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccCC
Q psy678 2 QRAQSLLKCENAAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDES 58 (60)
Q Consensus 2 ~~~~~~~e~~rnq~LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~~ 58 (60)
|-+......+|-+.|++.++++-...+ .+.++.-...++.++++. |+.+|+.|+.
T Consensus 498 Qa~~ar~r~~rT~~Lye~s~~L~~a~t-~~~vl~~~~~qi~~~~~~-~v~i~l~~~~ 552 (890)
T COG2205 498 QARAARRREQRTELLYEFSKKLAGART-REDILAAAGQQIASLLNQ-RVVILLPDDN 552 (890)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCC-HHHHHHHHHHHHHHHhCC-ceEEEEecCC
Confidence 445566677888999999999998777 999999999999999999 7999998865
No 14
>PF11849 DUF3369: Domain of unknown function (DUF3369); InterPro: IPR021800 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 170 amino acids in length.
Probab=58.54 E-value=46 Score=21.27 Aligned_cols=49 Identities=14% Similarity=0.322 Sum_probs=38.9
Q ss_pred HhHHHHHHH--HHHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheee
Q psy678 5 QSLLKCENA--AKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLL 54 (60)
Q Consensus 5 ~~~~e~~rn--q~LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslfl 54 (60)
...+|..|. +-.++.+..||+..+ +......|+.+...|++.+.-.++.
T Consensus 11 i~~Ie~~R~GLe~Ii~as~~L~~~~s-l~~fa~gvL~Ql~~Ll~~~~~~l~~ 61 (174)
T PF11849_consen 11 IRTIERNRQGLEKIIEASASLFQIRS-LQEFASGVLTQLSALLGLEDDGLYC 61 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCC-HHHHHHHHHHHHHHHhCCCCCeEEE
Confidence 344555555 678899999998555 9999999999999999998655555
No 15
>KOG3689|consensus
Probab=52.27 E-value=3.8 Score=32.68 Aligned_cols=26 Identities=31% Similarity=0.588 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHhhhccchhheeec
Q psy678 30 IEQVVVKIMQRAQSLLKCENAAVLLI 55 (60)
Q Consensus 30 id~li~~im~~a~~Ll~aeRcslflv 55 (60)
++...++++.+...+++|+||+.|++
T Consensus 7 ~~~~~~~~l~~~~~l~~a~r~~~f~~ 32 (707)
T KOG3689|consen 7 TEALCHKILQRVAGLLQADRCSLFLV 32 (707)
T ss_pred cccccchhhhhccccCCCCCcCeeee
Confidence 47788999999999999999999987
No 16
>smart00250 PLEC Plectin repeat.
Probab=51.62 E-value=7.1 Score=19.33 Aligned_cols=17 Identities=29% Similarity=0.368 Sum_probs=14.3
Q ss_pred hhhccchhheeeccCCC
Q psy678 43 SLLKCENAAVLLIDESS 59 (60)
Q Consensus 43 ~Ll~aeRcslflvD~~~ 59 (60)
.++.++.|+-+++|+.+
T Consensus 2 ~ll~~q~~~~Giidp~t 18 (38)
T smart00250 2 RLLEAQSAIGGIIDPET 18 (38)
T ss_pred ccchhhhheeEEEcCCC
Confidence 57888999999999865
No 17
>PF04406 TP6A_N: Type IIB DNA topoisomerase; InterPro: IPR013049 This entry represents the N-terminal domain found in Spo11, a meiotic recombination protein found in eukaryotes, and in subunit A of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea [, ]. These two types of proteins share structural homology. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Spo11 acts in conjunction with several other proteins, including Rec102 in yeast, to bring about meiotic recombination []. DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. They can be divided into two classes: type I enzymes (5.99.1.2 from EC, topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC, topoisomerases II, IV and VI) break double-strand DNA []. Topoisomerase VI is a type IIB enzymes that assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003824 catalytic activity, 0005524 ATP binding, 0006259 DNA metabolic process, 0005694 chromosome; PDB: 1D3Y_B 2ZBK_A 2Q2E_A.
Probab=46.02 E-value=19 Score=19.87 Aligned_cols=30 Identities=17% Similarity=0.361 Sum_probs=19.7
Q ss_pred HHhhhhccHHHHHHHHHHHHHhhhccchhheeec
Q psy678 22 DLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLI 55 (60)
Q Consensus 22 ~iFee~~sid~li~~im~~a~~Ll~aeRcslflv 55 (60)
.+|++|...|..+.+ +..++++.|-.+.++
T Consensus 39 ~lF~~Q~~vd~~i~d----i~~~l~~~R~~L~Iv 68 (68)
T PF04406_consen 39 SLFKSQREVDRAIDD----ICCLLGVSREDLNIV 68 (68)
T ss_dssp CS-SSHHHHHHHHHH----HHHHHTS-GGGGTEE
T ss_pred hhccCHHHHHHHHHH----HHHHHCCCHHHcCCC
Confidence 378888877776664 455788888877653
No 18
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=39.91 E-value=1.3e+02 Score=23.56 Aligned_cols=45 Identities=11% Similarity=0.189 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhhhh-ccHHHHHHHHHHHHHhhhccchhheeeccCC
Q psy678 14 AKLLEVVHDLFEEQ-TSIEQVVVKIMQRAQSLLKCENAAVLLIDES 58 (60)
Q Consensus 14 q~LL~la~~iFee~-~sid~li~~im~~a~~Ll~aeRcslflvD~~ 58 (60)
+.+.+++..+-... ...+..+...+..+..++.+++|.++++|..
T Consensus 277 ~~l~~l~~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~l~~~~ 322 (828)
T PRK13837 277 EVIAAISRCFEAASPHELEASIEAALGILAKFFDADSAALALVDVG 322 (828)
T ss_pred HHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHhCCCeeEEEEEcCC
Confidence 35555555543332 2235888889999999999999999999864
No 19
>COG2406 Protein distantly related to bacterial ferritins [General function prediction only]
Probab=39.33 E-value=12 Score=25.18 Aligned_cols=17 Identities=29% Similarity=0.350 Sum_probs=14.6
Q ss_pred HHHHHHHhhhccchhhe
Q psy678 36 KIMQRAQSLLKCENAAV 52 (60)
Q Consensus 36 ~im~~a~~Ll~aeRcsl 52 (60)
+++...+.++.||||.+
T Consensus 104 D~~~~l~vlv~AE~CAi 120 (172)
T COG2406 104 DIDEILAVLVKAERCAI 120 (172)
T ss_pred CHHHHHHHHHHHHHHHH
Confidence 47788889999999986
No 20
>COG2893 ManX Phosphotransferase system, mannose/fructose-specific component IIA [Carbohydrate transport and metabolism]
Probab=38.96 E-value=76 Score=20.27 Aligned_cols=46 Identities=24% Similarity=0.294 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHhhhhc-----------cHHHHHHHHHHHHHhhhccchhheeeccCC
Q psy678 13 AAKLLEVVHDLFEEQT-----------SIEQVVVKIMQRAQSLLKCENAAVLLIDES 58 (60)
Q Consensus 13 nq~LL~la~~iFee~~-----------sid~li~~im~~a~~Ll~aeRcslflvD~~ 58 (60)
-+-|+..++.||+++. +.++.+.+.+..+...+.++.-.+||.|-.
T Consensus 13 A~~l~~s~emi~G~q~nv~~v~~~~~~~~~~~l~~~~~~~~~~~d~~eevl~ltDl~ 69 (143)
T COG2893 13 AEGLLNSLEMILGEQENVEAVDFVPGEDSEDLLTKQIAAAIAALDSGEGVLFLTDLF 69 (143)
T ss_pred HHHHHHHHHHHhCcHhceEEEEeecCCChHHHHHHHHHHHHhhcCCCCcEEEEEecC
Confidence 4568899999999864 478889999999999999877899999864
No 21
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=36.41 E-value=71 Score=25.14 Aligned_cols=44 Identities=23% Similarity=0.514 Sum_probs=33.7
Q ss_pred HHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccCCC
Q psy678 15 KLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDESS 59 (60)
Q Consensus 15 ~LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~~~ 59 (60)
.+.++.+.+-.+. .++.++..+.....+|++|+...|...|.++
T Consensus 35 ~l~el~~~l~~~~-~~e~ll~~v~~~l~~~~~~~~~~ll~~d~~~ 78 (550)
T COG3604 35 ILVELTNALLSPL-RLERLLAEVAKELHSLFGCDASALLRLDSKN 78 (550)
T ss_pred HHHHhhhhhcCch-hHHHHHHHHHHHHHHHhcCCeeEEEEecccc
Confidence 5556666555544 4999999999999999999988888777653
No 22
>KOG0479|consensus
Probab=33.73 E-value=26 Score=28.47 Aligned_cols=29 Identities=24% Similarity=0.587 Sum_probs=21.5
Q ss_pred hhhhccHHHH-HHHHHHHH---------Hhhhccchhhee
Q psy678 24 FEEQTSIEQV-VVKIMQRA---------QSLLKCENAAVL 53 (60)
Q Consensus 24 Fee~~sid~l-i~~im~~a---------~~Ll~aeRcslf 53 (60)
|.-++++|+. ||++|.+- -.-||| ||||.
T Consensus 407 FDKMsDiDRvAIHEVMEQqtVTIaKAGIHasLNA-RCSVl 445 (818)
T KOG0479|consen 407 FDKMSDIDRVAIHEVMEQQTVTIAKAGIHASLNA-RCSVL 445 (818)
T ss_pred cccccchhHHHHHHHHhcceEEeEeccchhhhcc-ceeee
Confidence 6677888865 78888763 356788 89985
No 23
>PF06635 NolV: Nodulation protein NolV; InterPro: IPR010586 This family consists of several nodulation protein NolV sequences from different Rhizobium species []. The function of this family is unclear.; GO: 0009877 nodulation
Probab=27.72 E-value=2.1e+02 Score=19.77 Aligned_cols=45 Identities=24% Similarity=0.315 Sum_probs=37.3
Q ss_pred hHHhHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHhhhccc
Q psy678 3 RAQSLLKCENAAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCE 48 (60)
Q Consensus 3 ~~~~~~e~~rnq~LL~la~~iFee~~sid~li~~im~~a~~Ll~ae 48 (60)
++.-.+|+..-+..++.++.|.++.. -+.++.+...+|...+.-+
T Consensus 86 r~~a~LE~~l~~LVl~~Vr~ILg~fd-~~ell~r~vr~Al~~~~~~ 130 (207)
T PF06635_consen 86 RYLAGLEQELAELVLEIVRKILGEFD-PDELLVRAVRQALSQIRQG 130 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCC-hHHHHHHHHHHHHHHHhcC
Confidence 56777899999999999999999998 8888888887777665544
No 24
>PF08468 MTS_N: Methyltransferase small domain N-terminal; InterPro: IPR013675 This domain is found to the N terminus of the methyltransferase small domain (IPR007848 from INTERPRO) in bacterial proteins []. ; GO: 0008990 rRNA (guanine-N2-)-methyltransferase activity, 0006364 rRNA processing; PDB: 2PJD_A.
Probab=26.75 E-value=15 Score=23.65 Aligned_cols=29 Identities=7% Similarity=0.031 Sum_probs=19.5
Q ss_pred hhccHHHHHHHHHHHHHhhhccchhheeec
Q psy678 26 EQTSIEQVVVKIMQRAQSLLKCENAAVLLI 55 (60)
Q Consensus 26 e~~sid~li~~im~~a~~Ll~aeRcslflv 55 (60)
.+.|++.++... ..+.++=+|-||++|=.
T Consensus 110 GIkSa~K~L~~~-~~~~KiDSARhC~Ly~~ 138 (155)
T PF08468_consen 110 GIKSAEKQLAPY-GKINKIDSARHCSLYSG 138 (155)
T ss_dssp TGGGHHHHHTTT-S--EEE---TTEEEEEE
T ss_pred cHHHHHHHHHhh-CCcceeecccccEEEEE
Confidence 467888888887 67899999999999754
No 25
>COG5211 SSU72 RNA polymerase II-interacting protein involved in transcription start site selection [Transcription]
Probab=26.41 E-value=1.5e+02 Score=20.22 Aligned_cols=30 Identities=37% Similarity=0.460 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhhhhccHHHHHHHHHHHHHh
Q psy678 14 AKLLEVVHDLFEEQTSIEQVVVKIMQRAQS 43 (60)
Q Consensus 14 q~LL~la~~iFee~~sid~li~~im~~a~~ 43 (60)
+..|+++..+-++..-+|..+..||..-++
T Consensus 154 kaILelvd~L~~~~e~lE~~~~sil~~~qs 183 (197)
T COG5211 154 KAILELVDVLAKEEERLEYAVDSILRRYQS 183 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 678999999999999999999999987664
No 26
>PF10482 CtIP_N: Tumour-suppressor protein CtIP N-terminal domain; InterPro: IPR019518 CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control []. This N-terminal domain carries a coiled-coil region and is essential for homodimerisation of the protein []. The C-terminal domain is family CtIP_C and carries functionally important CxxC and RHR motifs, absence of which lead cells to grow slowly and show hypersensitivity to genotoxins [].
Probab=24.74 E-value=64 Score=20.62 Aligned_cols=6 Identities=33% Similarity=1.054 Sum_probs=4.7
Q ss_pred cchhhe
Q psy678 47 CENAAV 52 (60)
Q Consensus 47 aeRcsl 52 (60)
||||+|
T Consensus 70 CDRC~V 75 (120)
T PF10482_consen 70 CDRCTV 75 (120)
T ss_pred chHHHH
Confidence 788876
No 27
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=23.72 E-value=1.2e+02 Score=23.06 Aligned_cols=42 Identities=14% Similarity=0.234 Sum_probs=34.4
Q ss_pred HHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccCC
Q psy678 16 LLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDES 58 (60)
Q Consensus 16 LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~~ 58 (60)
++...+.+-+ ..+.+.++..++..+..+++++...+++.|.+
T Consensus 307 ~l~~~~~L~~-~~~~~~l~~~~~~~l~~~l~~~~g~l~l~~~~ 348 (679)
T TIGR02916 307 WLRFTQTLSE-ARSSDDLGERVIRALAQLVESPGGVLWLKSGN 348 (679)
T ss_pred HHHHHHHHhC-CCCCccHHHHHHHHHHHHhCCCCceEEEEcCC
Confidence 4667777744 45688999999999999999999999988754
No 28
>PF03523 Macscav_rec: Macrophage scavenger receptor; InterPro: IPR003543 The egg peptide speract receptor is a transmembrane glycoprotein of about 500 amino acids []. Topologically, it comprises a large extracellular domain of about 450 residues, followed by a transmembrane domain and a short cytoplasmic region of about 12 amino acids. The extracellular domain contains 4 repeats of a well-conserved region, which spans 115 amino acids and contains 6 conserved cysteines. A similar domain is also found towards the C terminus of macrophage scavenger receptor type I [], a membrane glycoprotein implicated in the pathologic deposition of cholesterol in arterial walls during artherogenesis, and in the CD5 glycoprotein, which acts as a receptor in regulating T-cell proliferation. The type I and type II human scavenger receptors are similar to their bovine, rabbit and murine counterparts. They consist of 6 domains: cytoplasmic (I); membrane-spanning (II); spacer (III); alpha-helical coiled- coil (IV); collagen-like (V); and a type-specific C-terminal (VI) []. Immunohistochemical studies have indicated the presence of scavenger receptors in the macrophages of lipid-rich atherosclerotic lesions, suggesting the involvement of these receptors in atherogenesis []. The macrophage scavenger receptor is trimeric and has unusual ligand-binding properties []. The trimeric structure of the bovine type I scavenger receptor contains 3 extracellular C-terminal cysteine-rich domains connected to the transmembrane domain by a long fibrous stalk. The stalk structure, which consists of an alpha-helical coiled coil and a collagen-like triple helix, has not previously been observed in an integral membrane protein []. ; GO: 0005044 scavenger receptor activity, 0006898 receptor-mediated endocytosis, 0016020 membrane
Probab=23.01 E-value=1.1e+02 Score=16.61 Aligned_cols=23 Identities=13% Similarity=-0.083 Sum_probs=17.0
Q ss_pred hhHHhHHHHHHHHHHHHHHHHHh
Q psy678 2 QRAQSLLKCENAAKLLEVVHDLF 24 (60)
Q Consensus 2 ~~~~~~~e~~rnq~LL~la~~iF 24 (60)
||-...-.++-|.+||.+...+.
T Consensus 22 qNfS~~TDQRfnDvllQl~sl~s 44 (49)
T PF03523_consen 22 QNFSMTTDQRFNDVLLQLNSLVS 44 (49)
T ss_pred cccchhhHHHHHHHHHHHHHHHH
Confidence 56666777888999998776553
No 29
>PF08256 Antimicrobial20: Aurein-like antibiotic peptide; InterPro: IPR013157 This family of antibacterial peptides are secreted from the granular dorsal glands of Litoria aurea (Green and golden bell frog), Litoria raniformis (Southern bell frog), Litoria citropa (Australian blue mountains tree frog) and frogs from genus Uperoleia. They are a part of the FSAP peptide family. Amongst the more active of these are aurein 1.2, aurein 2.2 and aurein 3.1; caerin 1.1, maculatin 1.1, uperin 3.6 []; citropin 1.1, citropin 1.2, citropin 1.3 and a minor peptide are wide-spectrum antibacterial peptides [].; GO: 0006952 defense response
Probab=22.32 E-value=74 Score=12.91 Aligned_cols=10 Identities=10% Similarity=0.471 Sum_probs=6.4
Q ss_pred HHHHHHHHhh
Q psy678 16 LLEVVHDLFE 25 (60)
Q Consensus 16 LL~la~~iFe 25 (60)
|++.++++++
T Consensus 2 l~Di~Kkv~g 11 (13)
T PF08256_consen 2 LFDIAKKVVG 11 (13)
T ss_pred HHHHHHHHhc
Confidence 5666777664
No 30
>PF02283 CobU: Cobinamide kinase / cobinamide phosphate guanyltransferase; InterPro: IPR003203 This family is composed of a group of bifunctional cobalbumin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity. The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape [].; GO: 0000166 nucleotide binding, 0043752 adenosylcobinamide kinase activity, 0051188 cofactor biosynthetic process; PDB: 1CBU_C 1C9K_B.
Probab=22.22 E-value=2e+02 Score=18.48 Aligned_cols=41 Identities=20% Similarity=0.310 Sum_probs=24.8
Q ss_pred HHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccC
Q psy678 16 LLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDE 57 (60)
Q Consensus 16 LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~ 57 (60)
-+|+++.+|.+-.+-+.+...+......+-+.. +.+++|-+
T Consensus 82 t~wl~n~l~~~~~~~~~~~~~i~~~l~~l~~~~-~~lViVsn 122 (167)
T PF02283_consen 82 TLWLANLLFAEEDDEEDILEEIERLLEALRERN-ADLVIVSN 122 (167)
T ss_dssp HHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH---SEEEEEEE
T ss_pred HHHHHHHHHhccCcHHHHHHHHHHHHHHHHccC-CCEEEEEc
Confidence 478999999987654555555555555554443 55665543
No 31
>PF04793 Herpes_BBRF1: BRRF1-like protein; InterPro: IPR006878 Most proteins in this entry are uncharacterised viral proteins translated from gene 49. The UL6 locus of pseudorabies virus (PRV) has a gene cluster with homology to herpes simplex virus UL5, UL6, UL7 and UL8, Epstein-Barr virus BBRF1 and BBRF2, and Kaposi sarcoma-associated herpes virus ORF43 and ORF42 [].
Probab=21.94 E-value=2.2e+02 Score=20.48 Aligned_cols=35 Identities=26% Similarity=0.221 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHhh
Q psy678 10 CENAAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSL 44 (60)
Q Consensus 10 ~~rnq~LL~la~~iFee~~sid~li~~im~~a~~L 44 (60)
-+|.++|+.+.+.+++...+=..++.+|...+.-.
T Consensus 32 leR~~fL~kv~q~L~qhr~~E~~Ivp~i~~ni~y~ 66 (284)
T PF04793_consen 32 LERGLFLLKVCQVLMQHRQSEPFIVPKIRSNIIYF 66 (284)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH
Confidence 67999999999999999888788888876665443
No 32
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=21.37 E-value=2.1e+02 Score=23.45 Aligned_cols=44 Identities=9% Similarity=0.261 Sum_probs=37.6
Q ss_pred HHHHHHHHhhhhccHHHHHHHHHHHHHhhhccchhheeeccCCC
Q psy678 16 LLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDESS 59 (60)
Q Consensus 16 LL~la~~iFee~~sid~li~~im~~a~~Ll~aeRcslflvD~~~ 59 (60)
+...|..-.+...++..++..+...+++.++-||.-+|=.|++.
T Consensus 134 ~~k~a~~~lq~a~~l~~l~~~~tqeVr~~tGfDRVMlYrF~~d~ 177 (750)
T COG4251 134 LAKLAMNRLQSAANLRDLLSRTTQEVRRMTGFDRVMLYRFDEDG 177 (750)
T ss_pred HHHHHHHHHhcCccHHHHHHHHHHHHHHhcCCceEEEEeecCCC
Confidence 34556666788999999999999999999999999998888765
No 33
>PF00681 Plectin: Plectin repeat; InterPro: IPR001101 Plectin may have a role in cross-linking intermediate filaments, in inter-linking intermediate filaments with microtubules and microfilaments and in anchoring intermediate filaments to the plasma and nuclear membranes. Plectin is recruited into hemidesmosomes, multiprotein complexes that facilitate adhesion of epithelia to the basement membrane, thereby providing linkage between the intracellular keratin filaments to the laminins of the extracellular matrix. Plectin binds to hemidesmosomes through association of its actin-binding domain with the first pair of fibronectin type III repeats and a small part of the connecting segment of the integrin-beta4 subunit, the latter (integrin-alpha6,beta4) acting as a receptor for the extracellular matrix component laminin-5. The plectin repeat is also seen in the cell adhesion junction plaque proteins, desmoplakin, envoplakin, and bullous pemphigoid antigen. The domains in plakins show considerable sequence homology. The N terminus consists of a plakin domain containing a number of subdomains with high alpha-helical content, while the central coiled-coil domain is composed of heptad repeats involved in the dimerisation of plakin, and the C terminus contains one or more homologous repeat sequences referred to plectin repeats []. This entry represents the plectin repeats found in the C terminus of plakin proteins.; GO: 0005856 cytoskeleton; PDB: 1LM7_A 1LM5_A.
Probab=21.17 E-value=41 Score=17.12 Aligned_cols=17 Identities=29% Similarity=0.319 Sum_probs=13.5
Q ss_pred hhhccchhheeeccCCC
Q psy678 43 SLLKCENAAVLLIDESS 59 (60)
Q Consensus 43 ~Ll~aeRcslflvD~~~ 59 (60)
.++.|+.|+=.++|+.+
T Consensus 2 rlLe~Q~~~gGiidp~t 18 (45)
T PF00681_consen 2 RLLEAQLATGGIIDPET 18 (45)
T ss_dssp HHHHHHHTTTSEEETTT
T ss_pred ceeeeeeeeeeEEeCCC
Confidence 47788888888888865
No 34
>KOG4422|consensus
Probab=20.52 E-value=82 Score=24.88 Aligned_cols=34 Identities=21% Similarity=0.214 Sum_probs=29.3
Q ss_pred HHHHHHhhhhccHHHHHHHHHHHHHhhhccchhh
Q psy678 18 EVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAA 51 (60)
Q Consensus 18 ~la~~iFee~~sid~li~~im~~a~~Ll~aeRcs 51 (60)
++|..+||-.+.-|.-+.-+.+-..++.+|||..
T Consensus 194 ~vAdL~~E~~PKT~et~s~mI~Gl~K~~~~ERA~ 227 (625)
T KOG4422|consen 194 AVADLLFETLPKTDETVSIMIAGLCKFSSLERAR 227 (625)
T ss_pred cHHHHHHhhcCCCchhHHHHHHHHHHHHhHHHHH
Confidence 4788999999988888888888888999999975
Done!