Query 027312
Match_columns 225
No_of_seqs 125 out of 209
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 08:03:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027312.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027312hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2351 RNA polymerase II, fou 100.0 1.2E-41 2.5E-46 275.4 9.2 130 91-224 3-132 (134)
2 COG5250 RPB4 RNA polymerase II 100.0 2.8E-32 6.1E-37 219.8 9.6 131 91-224 4-136 (138)
3 smart00657 RPOL4c DNA-directed 100.0 2.5E-31 5.4E-36 212.0 11.4 116 104-224 1-116 (118)
4 PRK14981 DNA-directed RNA poly 99.9 1.2E-26 2.5E-31 184.5 10.3 105 109-224 8-112 (112)
5 PF03874 RNA_pol_Rpb4: RNA pol 99.9 1.6E-26 3.5E-31 181.4 9.6 110 112-223 1-117 (117)
6 COG1460 Uncharacterized protei 99.6 2E-14 4.4E-19 115.3 10.5 105 109-225 9-114 (114)
7 KOG4168 Predicted RNA polymera 98.6 6.7E-08 1.5E-12 80.7 6.6 113 108-222 6-130 (149)
8 PF06569 DUF1128: Protein of u 87.5 1.2 2.5E-05 33.6 4.4 40 185-224 32-71 (71)
9 PF11459 DUF2893: Protein of u 60.4 9.3 0.0002 28.5 2.7 38 183-223 10-49 (69)
10 COG2511 GatE Archaeal Glu-tRNA 57.0 39 0.00084 34.6 7.1 78 139-220 498-582 (631)
11 COG4840 Uncharacterized protei 53.3 16 0.00034 27.5 2.9 35 190-224 37-71 (71)
12 PF00619 CARD: Caspase recruit 49.1 45 0.00097 23.9 4.8 55 163-221 18-73 (85)
13 cd01106 HTH_TipAL-Mta Helix-Tu 43.2 1.3E+02 0.0029 22.7 6.9 57 160-222 41-99 (103)
14 PF09868 DUF2095: Uncharacteri 42.2 27 0.00058 29.0 2.9 32 188-219 74-105 (128)
15 PF11829 DUF3349: Protein of u 40.2 71 0.0015 25.3 4.9 79 141-221 2-87 (96)
16 PRK10391 oriC-binding nucleoid 38.2 44 0.00095 25.3 3.3 34 147-181 3-37 (71)
17 PRK10945 gene expression modul 36.4 43 0.00093 25.4 3.0 35 146-181 7-41 (72)
18 PF07299 FBP: Fibronectin-bind 35.7 26 0.00056 31.1 2.1 69 143-222 10-78 (208)
19 PF06207 DUF1002: Protein of u 35.2 46 0.001 29.8 3.6 43 182-224 165-209 (225)
20 PF00570 HRDC: HRDC domain Blo 33.5 18 0.0004 25.0 0.6 24 174-197 26-49 (68)
21 TIGR01878 cas_Csa5 CRISPR-asso 33.4 23 0.00051 28.2 1.2 68 144-220 4-78 (97)
22 KOG4479 Transcription factor e 32.3 85 0.0018 24.6 4.1 58 155-222 31-89 (92)
23 PF01152 Bac_globin: Bacterial 32.0 2.3E+02 0.005 21.6 6.8 77 137-224 35-115 (120)
24 CHL00181 cbbX CbbX; Provisiona 31.4 2E+02 0.0043 26.1 7.1 54 112-171 195-248 (287)
25 PF14771 DUF4476: Domain of un 31.3 2.1E+02 0.0045 21.4 6.2 59 143-203 9-71 (95)
26 KOG4204 Histone deacetylase co 30.4 4E+02 0.0087 23.9 9.0 104 113-224 17-160 (231)
27 PF13543 KSR1-SAM: SAM like do 30.0 29 0.00062 28.8 1.3 44 176-219 67-111 (129)
28 cd08325 CARD_CASP1-like Caspas 28.8 96 0.0021 23.2 3.9 58 161-221 16-74 (83)
29 PF04472 DUF552: Protein of un 28.3 43 0.00093 24.3 1.8 33 188-220 6-45 (73)
30 COG4003 Uncharacterized protei 27.5 45 0.00097 26.4 1.9 25 188-212 44-68 (98)
31 cd01671 CARD Caspase activatio 27.4 1.7E+02 0.0037 20.6 4.9 54 164-221 16-70 (80)
32 PF09999 DUF2240: Uncharacteri 26.9 94 0.002 26.2 3.9 42 142-183 85-127 (144)
33 KOG2759 Vacuolar H+-ATPase V1 25.8 64 0.0014 31.9 3.0 47 173-220 256-316 (442)
34 PF05635 23S_rRNA_IVP: 23S rRN 24.8 1.1E+02 0.0024 23.4 3.7 80 144-223 16-104 (110)
35 PF00034 Cytochrom_C: Cytochro 24.8 73 0.0016 21.7 2.5 17 207-223 75-91 (91)
36 PRK07168 bifunctional uroporph 24.2 75 0.0016 31.3 3.2 58 156-220 412-470 (474)
37 PF08535 KorB: KorB domain; I 24.0 58 0.0012 24.4 1.9 79 143-224 12-91 (93)
38 PF14762 HPS3_Mid: Hermansky-P 23.1 2.6E+02 0.0057 27.1 6.6 108 114-222 252-369 (374)
39 cd08315 Death_TRAILR_DR4_DR5 D 22.4 3.5E+02 0.0075 20.9 6.0 75 142-223 4-78 (96)
40 PF01465 GRIP: GRIP domain; I 22.1 54 0.0012 22.2 1.3 30 187-216 17-46 (46)
41 TIGR02880 cbbX_cfxQ probable R 22.1 3E+02 0.0065 24.8 6.5 55 112-172 194-248 (284)
42 COG1378 Predicted transcriptio 21.9 83 0.0018 28.3 2.8 33 164-196 3-38 (247)
43 PF09524 Phg_2220_C: Conserved 21.7 1.5E+02 0.0034 22.2 3.8 51 148-199 2-60 (74)
44 cd01109 HTH_YyaN Helix-Turn-He 21.4 2.1E+02 0.0045 22.0 4.7 40 160-199 41-85 (113)
45 COG3310 Uncharacterized protei 21.2 1.3E+02 0.0028 26.5 3.7 44 178-225 23-72 (196)
46 PRK09726 antitoxin HipB; Provi 21.0 2.2E+02 0.0047 21.0 4.5 53 161-219 12-64 (88)
47 PF09702 Cas_Csa5: CRISPR-asso 20.8 39 0.00085 27.3 0.4 73 144-221 4-87 (105)
48 TIGR02498 type_III_ssaH type I 20.8 2.4E+02 0.0051 21.8 4.6 57 143-199 21-79 (79)
No 1
>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]
Probab=100.00 E-value=1.2e-41 Score=275.44 Aligned_cols=130 Identities=35% Similarity=0.460 Sum_probs=123.8
Q ss_pred cccccCccccccCcccccccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Q 027312 91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSL 170 (225)
Q Consensus 91 ~~~eE~aaeLkLG~eF~~nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL 170 (225)
...|||||+|+||+||. ++.|||+|||++||+++.++.+ .+.|+..++++||.||+.|+++||||+|++++.+||++|
T Consensus 3 g~~EEdAa~lk~g~EFe-~~~~L~~sEa~lllE~~~~q~~-rs~d~~~~~s~Vf~kTl~Y~~~FsRfKn~etv~avr~iL 80 (134)
T KOG2351|consen 3 GEEEEDAAELKLGKEFE-TADALMLSEARLLLEHRLEQRR-RSEDDESEMSDVFKKTLQYLDRFSRFKNRETVRAVRTIL 80 (134)
T ss_pred chhhccHHhccccHHHH-HHHHHHHHHHHHHHHHHHHHHh-hcccccchHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 46899999999999998 9999999999999999998864 367888999999999999999999999999999999999
Q ss_pred hhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312 171 SEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS 224 (225)
Q Consensus 171 ~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~ 224 (225)
...+||+||+|||+||||+|+|||++|||||+.| ++|+.|++||++|+.+|.
T Consensus 81 s~~~lhkFE~A~lgnLcpetaEEAkaLvPSL~nk--idD~~le~iL~dls~lr~ 132 (134)
T KOG2351|consen 81 SGKGLHKFEVAQLGNLCPETAEEAKALVPSLENK--IDDDELEQILKDLSTLRT 132 (134)
T ss_pred hhCCcchhhHHHHhccCcccHHHHHHhccccccc--cCHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999999999998 999999999999999885
No 2
>COG5250 RPB4 RNA polymerase II, fourth largest subunit [Transcription]
Probab=99.97 E-value=2.8e-32 Score=219.80 Aligned_cols=131 Identities=24% Similarity=0.330 Sum_probs=117.2
Q ss_pred cccccCccccccCcccccccccccHHHHHHHHHHHHHHhhhhcCCCCCCchH--HHHHHHHHHHhcCCCCCHHHHHHHHH
Q 027312 91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPV--SFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (225)
Q Consensus 91 ~~~eE~aaeLkLG~eF~~nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~--Vf~KTleYl~rFSk~k~~esv~~Vre 168 (225)
+..|||||+|+|||||+ |...||++||+++|+....+++.+-.......++ +|++|+.|++.||+|++.+.+.+++.
T Consensus 4 ~~~ee~aa~lklg~efe-~ed~l~lsEAr~lie~~l~~rrretn~~e~~s~dvk~~k~T~~Yl~~F~Rfkd~e~~~a~~~ 82 (138)
T COG5250 4 AIFEEDAAQLKLGPEFE-NEDMLMLSEARYLIEGQLERRRRETNGAEFRSNDVKVFKSTLGYLDDFCRFKDKEVAEALRT 82 (138)
T ss_pred hHhhhhHHHhhcCcccc-chHHHHHHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 45799999999999998 9999999999999999887764221112333444 49999999999999999999999999
Q ss_pred HhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312 169 SLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS 224 (225)
Q Consensus 169 lL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~ 224 (225)
+|...|+|+||+||+++|||+++||||+|||||..| ++|..+|.||++++.+|+
T Consensus 83 ~L~~~gfh~fEiAqlGsL~c~saeEAktLiPSL~nk--idD~~lq~ilkels~l~~ 136 (138)
T COG5250 83 TLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNK--IDDAILQAILKELSLLRK 136 (138)
T ss_pred HHccCCcchhhHHHhhccccccHHHHHhhccccccc--ccHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999998 999999999999999986
No 3
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=99.97 E-value=2.5e-31 Score=211.96 Aligned_cols=116 Identities=28% Similarity=0.393 Sum_probs=105.3
Q ss_pred cccccccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhhh
Q 027312 104 QELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVI 183 (225)
Q Consensus 104 ~eF~~nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAqL 183 (225)
++|. |++|||||||++||+.++... .+.++..+++.|+++|++|+++|+++++++++.++++.|..++||+||+|||
T Consensus 1 ~~f~-~a~~L~n~Ev~~ll~~k~~~~--~~~~~~~~l~~v~~~tl~Yl~~~~~~~~~e~i~~~~~~L~~~~L~k~E~~~i 77 (118)
T smart00657 1 PEFK-NATCLTNSEVQLLLELKRQSK--ESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVRTLLKSKKLHKFEIAQL 77 (118)
T ss_pred CCcc-chhHhHHHHHHHHHHHHHHhh--ccccccchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCCHHHHHHH
Confidence 4787 999999999999999654322 2344556788999999999999999999999999999999999999999999
Q ss_pred hccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312 184 ANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS 224 (225)
Q Consensus 184 aNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~ 224 (225)
+||||+|++||++|||||++| |+|++|++||++|+++|.
T Consensus 78 ~Nl~P~s~~E~~~lI~sl~~r--~~ee~l~~iL~~i~~~~~ 116 (118)
T smart00657 78 GNLRPETAEEAQLLIPSLEER--IDEEELEELLDDLSSLLP 116 (118)
T ss_pred hCCCCCCHHHHHHHhhhhhcc--CCHHHHHHHHHHHHHhcC
Confidence 999999999999999999987 999999999999999985
No 4
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=99.94 E-value=1.2e-26 Score=184.50 Aligned_cols=105 Identities=23% Similarity=0.277 Sum_probs=92.6
Q ss_pred ccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhhhhccCC
Q 027312 109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICP 188 (225)
Q Consensus 109 nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAqLaNL~P 188 (225)
..+|||++||+.||+++.+.. ++++++++|++|+++|++++..++.+.+++++...+|++|++|+|+||||
T Consensus 8 ~e~~lt~sEa~~iL~~~~~~~---------els~~~~ktl~y~~kFsk~~~e~a~elve~L~~~~~l~e~~a~~I~nL~P 78 (112)
T PRK14981 8 EEEYITIAEAKEILSEIEEER---------ELSYELRRTLDYLNRFSKLDPEDAEELVEELLELEKMKEKTAVKIADILP 78 (112)
T ss_pred hcccccHHHHHHHHHHHHhcc---------chhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHccCCCHHHHHHHHhcCC
Confidence 567999999999999876531 67899999999999999997666777666777777799999999999999
Q ss_pred CCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312 189 ETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS 224 (225)
Q Consensus 189 eT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~ 224 (225)
+|+||||+|||++.. ++++++|++|||+|.+||.
T Consensus 79 ~~~dElrai~~~~~~--~~~~e~l~~ILd~l~k~~~ 112 (112)
T PRK14981 79 ETRDELRAIFAKERY--TLSPEELDEILDIVKKYRE 112 (112)
T ss_pred CCHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhhC
Confidence 999999999999844 5999999999999999973
No 5
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=99.94 E-value=1.6e-26 Score=181.37 Aligned_cols=110 Identities=32% Similarity=0.416 Sum_probs=93.9
Q ss_pred cccHHHHHHHHHHHHHHhhhh-------cCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhhhh
Q 027312 112 CLMDCEAAHILEGIQEQMALL-------SADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIA 184 (225)
Q Consensus 112 cLsnsEV~~ILe~~~e~~~~~-------s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAqLa 184 (225)
||||+||+.||+++.+..... ...+..+++.++++|++|+++|+++++++++..+++.|..++|+++|++||+
T Consensus 1 ~Lsn~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Yl~~~~~~~~~e~~~~l~~~L~~~~L~~~E~~qi~ 80 (117)
T PF03874_consen 1 LLSNYEVLQILEKRREEQKNKSKKKQKNKEDPPENLNTIQYKTLEYLEKFSKFQNPESIKELREELKKFGLTEFEILQII 80 (117)
T ss_dssp EE-HHHHHHHHHHHHHHHHCHCHHHHHHHHHCSSCHCHHHHHHHHHHHHH-SSSSHHHHHHHHHHHTTSTS-HHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHHHHHccccCCCHHHHHHHHHHHhcccCCHHHHHHHh
Confidence 799999999999655433211 1245678889999999999999999999999999999999999999999999
Q ss_pred ccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhh
Q 027312 185 NICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFK 223 (225)
Q Consensus 185 NL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r 223 (225)
||||+|++|+++|||+++.| |+|++|++||++|++||
T Consensus 81 Nl~P~~~~El~~ii~~~~~r--~~ee~l~~iL~~v~~~~ 117 (117)
T PF03874_consen 81 NLRPTTAVELRAIIESLESR--FSEEDLEEILDLVSKYR 117 (117)
T ss_dssp HH--SSHHHHHHHSTTGTTT--STHHHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHHHhccC--CCHHHHHHHHHHHHHhC
Confidence 99999999999999999986 99999999999999987
No 6
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=99.57 E-value=2e-14 Score=115.32 Aligned_cols=105 Identities=20% Similarity=0.316 Sum_probs=85.8
Q ss_pred ccccccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhh-CCCCchhhhhhhccC
Q 027312 109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSE-HGVTDGEICVIANIC 187 (225)
Q Consensus 109 nakcLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~-~~L~kfEiAqLaNL~ 187 (225)
+-+.+|++||+.||..+ ....++++.++.||+|+++|+++. |+.++++.+-|.. .++.+.-++-|+.||
T Consensus 9 e~~yiti~Eak~il~~~---------~~~~eL~y~~~~al~y~~kFakld-pe~a~e~veEL~~i~~~~e~~avkIadI~ 78 (114)
T COG1460 9 EEKYITISEAKKILSKV---------EREEELTYEQREALEYAEKFAKLD-PEKARELVEELLSIVKMSEKIAVKIADIM 78 (114)
T ss_pred hccCccHHHHHHHHHHh---------cccccchHHHHHHHHHHHHHhcCC-HHHHHHHHHHHHhhccccHHHHHHHHHhC
Confidence 44689999999999977 233567899999999999999997 7777777766654 445444355599999
Q ss_pred CCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhcC
Q 027312 188 PETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST 225 (225)
Q Consensus 188 PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~~ 225 (225)
|+|.+|+|+|+.+ ++..+++|+|++|||.+.+||.+
T Consensus 79 P~t~~ElRsIla~--e~~~~s~E~l~~Ildiv~Ky~~~ 114 (114)
T COG1460 79 PRTPDELRSILAK--ERVMLSDEELDKILDIVDKYREE 114 (114)
T ss_pred CCCHHHHHHHHHH--ccCCCCHHHHHHHHHHHHHHhcC
Confidence 9999999999995 44578999999999999999863
No 7
>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]
Probab=98.64 E-value=6.7e-08 Score=80.73 Aligned_cols=113 Identities=18% Similarity=0.224 Sum_probs=91.3
Q ss_pred cccccccHHHHHHHHHHHHHHhhh--h-c-CCCC-----CCchHHHHHHHHHHHhc--CCCCCHHHHHHHHHHhhhCCCC
Q 027312 108 KNAKCLMDCEAAHILEGIQEQMAL--L-S-ADPT-----IKIPVSFDKGLLYAKTH--SHFTNPQAVKGLFQSLSEHGVT 176 (225)
Q Consensus 108 ~nakcLsnsEV~~ILe~~~e~~~~--~-s-~d~~-----~~~s~Vf~KTleYl~rF--Sk~k~~esv~~VrelL~~~~L~ 176 (225)
.+.-.|+|.||...|.....+... + + +... .+++.+.+.|+.|+..= +.-.++|.+.++..-+..++|+
T Consensus 6 ar~a~LtnyEVl~fL~el~~~n~~~~k~s~r~~~Q~~~~~~l~ti~~et~kYls~~~n~~~qt~E~i~el~~k~~~fkLt 85 (149)
T KOG4168|consen 6 ARNAALTNYEVLQFLNELECMNEEADKSSHRLGAQNILQNDLPTITYETLKYLSDNKNASTQTNESIIELITKLKSFKLT 85 (149)
T ss_pred hhHHHhhhHHHHHHHHHhhhhhhhhhhhhhhhhcccccccccchhHHHHHHHHhcCcccccccHHHHHHHHHHhccccch
Confidence 355689999999999887632110 0 0 1111 34788999999999983 5666788888888888999999
Q ss_pred chhhhhhhccCCCCHHHHHHhhccccccCCC-CHHHHHHHHHHHHhh
Q 027312 177 DGEICVIANICPETVEEAYAIVPSLKAKRSR-LNDLLKEVLIQLAKF 222 (225)
Q Consensus 177 kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~-~de~Lq~ILd~Lsk~ 222 (225)
+.|+.||.|+.|-++-|...+|.-+++| | ++++|.++|..+..+
T Consensus 86 KAE~LqiiN~rPss~vel~~~iE~~eeR--f~~ee~i~elv~~i~~~ 130 (149)
T KOG4168|consen 86 KAEILQIINLRPSSSVELYLIIEEVEER--FQDEEDIEELVETISKT 130 (149)
T ss_pred HHHHHHHhccCcchHHHHHHHHHHHHHh--ccchhcHHHHHHhcccc
Confidence 9999999999999999999999999987 7 999999999888653
No 8
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=87.47 E-value=1.2 Score=33.60 Aligned_cols=40 Identities=15% Similarity=0.195 Sum_probs=33.8
Q ss_pred ccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312 185 NICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS 224 (225)
Q Consensus 185 NL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~ 224 (225)
++-....|+.+-|+.....|.+|+..+++.|.++|.++|+
T Consensus 32 ~f~~~~yedl~diy~~V~~K~~fS~sEm~aI~~ELG~LRK 71 (71)
T PF06569_consen 32 DFSEEKYEDLKDIYEMVMSKDSFSPSEMQAIAEELGQLRK 71 (71)
T ss_pred hCChhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHhhcC
Confidence 4455668888888887777778999999999999999996
No 9
>PF11459 DUF2893: Protein of unknwon function (DUF2893); InterPro: IPR021561 This is a bacterial family of uncharacterised proteins.
Probab=60.43 E-value=9.3 Score=28.54 Aligned_cols=38 Identities=24% Similarity=0.350 Sum_probs=30.2
Q ss_pred hhccCCC--CHHHHHHhhccccccCCCCHHHHHHHHHHHHhhh
Q 027312 183 IANICPE--TVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFK 223 (225)
Q Consensus 183 LaNL~Pe--T~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r 223 (225)
+.+.+|+ +.+||+.|+.+|.. +....||++|+.-.+++
T Consensus 10 ~l~~~p~~~s~e~a~~l~egL~n---Lrp~~lq~LL~~C~svK 49 (69)
T PF11459_consen 10 LLSEVPKRQSFEEADELMEGLRN---LRPRVLQELLEHCTSVK 49 (69)
T ss_pred HHHhCCccCCHHHHHHHHHHHhh---cCHHHHHHHHHHCccHH
Confidence 6677776 57899999998874 88999999998766654
No 10
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=56.99 E-value=39 Score=34.55 Aligned_cols=78 Identities=13% Similarity=0.194 Sum_probs=52.7
Q ss_pred CchHHHHHHHHHHHhc-CCC--CCHHHHHHHHHHhhhCCCCchhhhh-hhccC--CC-CHHHHHHhhccccccCCCCHHH
Q 027312 139 KIPVSFDKGLLYAKTH-SHF--TNPQAVKGLFQSLSEHGVTDGEICV-IANIC--PE-TVEEAYAIVPSLKAKRSRLNDL 211 (225)
Q Consensus 139 ~~s~Vf~KTleYl~rF-Sk~--k~~esv~~VrelL~~~~L~kfEiAq-LaNL~--Pe-T~eEAkaLIPSLk~K~~~~de~ 211 (225)
-+..++..|+.|+++= ... -+.+-+..+..++....+.+.-+.. |..|| |. +++|+...+- |.. ++.|+
T Consensus 498 ~~A~~L~~~~~~L~reg~~i~~l~~~~i~~~~~~~~~g~iake~iee~l~~l~~~p~~~~~e~~~~~g-L~~---ls~eE 573 (631)
T COG2511 498 LIASTLVNTLPELRREGVEIDNLDDEHIEELLRLVSEGKIAKEAIEEILKALAENPGKDAAEIAEKLG-LKE---LSEEE 573 (631)
T ss_pred HHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHhcccchHHHHHHHHHHHHhCCCCCHHHHHHHhc-ccc---CCHHH
Confidence 3456788899999983 222 1355666666666666777655444 66777 54 6777776664 333 79999
Q ss_pred HHHHHHHHH
Q 027312 212 LKEVLIQLA 220 (225)
Q Consensus 212 Lq~ILd~Ls 220 (225)
++.|++.|-
T Consensus 574 ve~iI~eii 582 (631)
T COG2511 574 VEKIIDEII 582 (631)
T ss_pred HHHHHHHHH
Confidence 999998875
No 11
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.32 E-value=16 Score=27.49 Aligned_cols=35 Identities=14% Similarity=0.190 Sum_probs=30.3
Q ss_pred CHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312 190 TVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS 224 (225)
Q Consensus 190 T~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~ 224 (225)
..++..-|+-.+++|-+|+..+.|.|-++|.++|+
T Consensus 37 ~~edLtdiy~mvkkkenfSpsEmqaiA~eL~rlRk 71 (71)
T COG4840 37 NYEDLTDIYDMVKKKENFSPSEMQAIADELGRLRK 71 (71)
T ss_pred cHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhC
Confidence 46777888887777778999999999999999996
No 12
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=49.10 E-value=45 Score=23.93 Aligned_cols=55 Identities=18% Similarity=0.183 Sum_probs=41.6
Q ss_pred HHHHHHHhh-hCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHh
Q 027312 163 VKGLFQSLS-EHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAK 221 (225)
Q Consensus 163 v~~VrelL~-~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk 221 (225)
+..|...|. +.-|+..|...|-+ +|...+-++.||-.|.+| .+.....+++.|.+
T Consensus 18 ~~~ild~L~~~~vlt~~e~e~I~~-~~t~~~k~~~LLd~l~~k---g~~a~~~F~~~L~~ 73 (85)
T PF00619_consen 18 LDDILDHLLSRGVLTEEEYEEIRS-EPTRQDKARKLLDILKRK---GPEAFDIFCQALRE 73 (85)
T ss_dssp HHHHHHHHHHTTSSSHHHHHHHHT-SSSHHHHHHHHHHHHHHC---CHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHc-cCChHHHHHHHHHHHHHH---CHHHHHHHHHHHHh
Confidence 334444444 44588888887887 999999999999999887 78888888777765
No 13
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=43.19 E-value=1.3e+02 Score=22.74 Aligned_cols=57 Identities=18% Similarity=0.116 Sum_probs=32.0
Q ss_pred HHHHHHHHH--HhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhh
Q 027312 160 PQAVKGLFQ--SLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKF 222 (225)
Q Consensus 160 ~esv~~Vre--lL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~ 222 (225)
++.+..++. .|...|++=.+|..+...++ +++..++-.-. ..-++++.++-..+..+
T Consensus 41 ~~di~~l~~i~~lr~~g~~l~~i~~~~~~~~---~~~~~~l~~~~---~~l~~~i~~l~~~~~~l 99 (103)
T cd01106 41 EEDLERLQQILFLKELGFSLKEIKELLKDPS---EDLLEALREQK---ELLEEKKERLDKLIKTI 99 (103)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHcCc---HHHHHHHHHHH---HHHHHHHHHHHHHHHHH
Confidence 455555543 34567888777777776665 66666665311 12344555544444444
No 14
>PF09868 DUF2095: Uncharacterized protein conserved in archaea (DUF2095); InterPro: IPR018662 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=42.18 E-value=27 Score=28.99 Aligned_cols=32 Identities=25% Similarity=0.191 Sum_probs=19.9
Q ss_pred CCCHHHHHHhhccccccCCCCHHHHHHHHHHH
Q 027312 188 PETVEEAYAIVPSLKAKRSRLNDLLKEVLIQL 219 (225)
Q Consensus 188 PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~L 219 (225)
|+|.+||.-+|--|..+..++.+....+-..|
T Consensus 74 C~T~EEALEVInylek~GEIt~e~A~eLr~~L 105 (128)
T PF09868_consen 74 CKTDEEALEVINYLEKRGEITPEEAKELRSIL 105 (128)
T ss_pred hCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 56666776666666666666666555554444
No 15
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=40.16 E-value=71 Score=25.26 Aligned_cols=79 Identities=15% Similarity=0.133 Sum_probs=48.6
Q ss_pred hHHHHHHHHHHHh-cCCCCCHHHHHHHHHHhhhCCCCchhhhhhhcc------CCCCHHHHHHhhccccccCCCCHHHHH
Q 027312 141 PVSFDKGLLYAKT-HSHFTNPQAVKGLFQSLSEHGVTDGEICVIANI------CPETVEEAYAIVPSLKAKRSRLNDLLK 213 (225)
Q Consensus 141 s~Vf~KTleYl~r-FSk~k~~esv~~VrelL~~~~L~kfEiAqLaNL------~PeT~eEAkaLIPSLk~K~~~~de~Lq 213 (225)
+..+.+.+++++. |-.-=....---+..+|.+ .|++.|+.+++.- .|.|.+++..+|-..-.. .-++++|.
T Consensus 2 ~~~l~~iv~WLRaGYP~GvP~~Dy~PLlALL~r-~Ltd~ev~~Va~~L~~~~~~~~~~~dI~~~I~~vt~~-~P~~~di~ 79 (96)
T PF11829_consen 2 PSFLASIVDWLRAGYPEGVPPTDYVPLLALLRR-RLTDDEVAEVAAELAARGDPPVDRIDIGVAITRVTDE-LPTPEDIE 79 (96)
T ss_dssp HHHHHHHHHHHHHH-TT-B-HHHHHHHHHHHTT-TS-HHHHHHHHHHHHHHTSS-BSCCHHHHHHHHHCSS--S-HHHHH
T ss_pred ChHHHHHHHHHHccCCCCCCCCccHHHHHHhcc-cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHcC-CcCHHHHH
Confidence 3556777777776 3332234444557777776 4999998776633 244788888888765553 34788999
Q ss_pred HHHHHHHh
Q 027312 214 EVLIQLAK 221 (225)
Q Consensus 214 ~ILd~Lsk 221 (225)
.+..-|..
T Consensus 80 RV~~~Laa 87 (96)
T PF11829_consen 80 RVRARLAA 87 (96)
T ss_dssp HHHHHHHT
T ss_pred HHHHHHHh
Confidence 88887764
No 16
>PRK10391 oriC-binding nucleoid-associated protein; Provisional
Probab=38.19 E-value=44 Score=25.27 Aligned_cols=34 Identities=24% Similarity=0.292 Sum_probs=27.2
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhhhCCCCc-hhhh
Q 027312 147 GLLYAKTHSHFTNPQAVKGLFQSLSEHGVTD-GEIC 181 (225)
Q Consensus 147 TleYl~rFSk~k~~esv~~VrelL~~~~L~k-fEiA 181 (225)
..+|+=+|-+|.+.++.+.|-+-+. +.|+. -|+.
T Consensus 3 k~eyLlkfRkcss~eTLEkv~e~~~-y~L~~~~e~~ 37 (71)
T PRK10391 3 VQDYLLKFRKISSLESLEKLFDHLN-YTLTDDQEII 37 (71)
T ss_pred HHHHHHHHHhcCcHHHHHHHHHHhh-cccCCHHHHH
Confidence 5799999999999999999988876 46665 4443
No 17
>PRK10945 gene expression modulator; Provisional
Probab=36.37 E-value=43 Score=25.37 Aligned_cols=35 Identities=9% Similarity=0.112 Sum_probs=28.0
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhh
Q 027312 146 KGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEIC 181 (225)
Q Consensus 146 KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiA 181 (225)
...+|+=+|-+|.+.++.+.|-+-+. +.|+.-|+.
T Consensus 7 tk~dyL~~fRrcss~eTLEkvie~~~-~~L~~~E~~ 41 (72)
T PRK10945 7 TKTDYLMRLRRCQTIDTLERVIEKNK-YELSDDELA 41 (72)
T ss_pred cHHHHHHHHHhcCcHHHHHHHHHHhh-ccCCHHHHH
Confidence 44899999999999999999988765 467665543
No 18
>PF07299 FBP: Fibronectin-binding protein (FBP); InterPro: IPR010841 This entry consists of several bacterial fibronectin-binding proteins which are thought to be involved in virulence in Listeria species [,].; PDB: 4ADO_B 4ADN_B 2YB5_F.
Probab=35.75 E-value=26 Score=31.15 Aligned_cols=69 Identities=13% Similarity=0.194 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhh
Q 027312 143 SFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKF 222 (225)
Q Consensus 143 Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~ 222 (225)
+=+++..-++.+....++..+++|+.+... -|.+++|+-.+|.+.|+..|... -+.++.+.+|+.|..|
T Consensus 10 Ik~q~~~L~~~~~tvnD~~vi~a~~~~~~~---------ki~~~f~~~~~eq~~ll~~i~~i--~~~~~~~~~L~~L~~y 78 (208)
T PF07299_consen 10 IKKQVYQLVNAYRTVNDPKVIEAVKSLAIE---------KILELFPELTEEQKELLEQIMDI--KTREEAEKYLEELKPY 78 (208)
T ss_dssp HHHHHHHHHHHHHC-T-CCCCHHHHHHHHH---------HHHHHHCTTTHHHCCHHHHHTST--T-HHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHhccCCHHHHHHHHHHHHH---------HHHHHcccCCHHHHHHHHHHhcc--CCHHHHHHHHHHHHHH
Confidence 344455555556666666666666654331 24445555555555555544442 1455555555555433
No 19
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=35.19 E-value=46 Score=29.84 Aligned_cols=43 Identities=19% Similarity=0.257 Sum_probs=35.7
Q ss_pred hhhccCCCCHHHHHHhhcccccc--CCCCHHHHHHHHHHHHhhhc
Q 027312 182 VIANICPETVEEAYAIVPSLKAK--RSRLNDLLKEVLIQLAKFKS 224 (225)
Q Consensus 182 qLaNL~PeT~eEAkaLIPSLk~K--~~~~de~Lq~ILd~Lsk~r~ 224 (225)
+|+.--|.|.+|++.+|--.... ..+++++++.|.+.+.+|+.
T Consensus 165 ~va~~~~~t~~eI~~IV~~~~~~~~i~ls~~q~~~i~~l~~~~~~ 209 (225)
T PF06207_consen 165 EVAKQKPKTDEEIRNIVNNVLNNYNINLSDEQIQQIVNLMKKIQN 209 (225)
T ss_pred HHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHc
Confidence 47788899999999999755443 36799999999999999875
No 20
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=33.45 E-value=18 Score=25.00 Aligned_cols=24 Identities=29% Similarity=0.380 Sum_probs=18.1
Q ss_pred CCCchhhhhhhccCCCCHHHHHHh
Q 027312 174 GVTDGEICVIANICPETVEEAYAI 197 (225)
Q Consensus 174 ~L~kfEiAqLaNL~PeT~eEAkaL 197 (225)
-|++..+..||...|.|++|...+
T Consensus 26 Il~~~~L~~ia~~~P~s~~~L~~i 49 (68)
T PF00570_consen 26 ILSDEALLEIAKRLPTSIEELLQI 49 (68)
T ss_dssp HS-HHHHHHHHHH--SSHHHHHTS
T ss_pred ccCHHHHHHHHHhCCCCHHHHHHc
Confidence 466677888999999999999998
No 21
>TIGR01878 cas_Csa5 CRISPR-associated protein, Csa5 family. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model represents a minor family of Cas protein found in the (all archaeal) APERN subtype of CRISPR/Cas locus, so the family is designated Csa5, for CRISPR/Cas Subtype Protein 5.
Probab=33.39 E-value=23 Score=28.18 Aligned_cols=68 Identities=16% Similarity=0.154 Sum_probs=38.8
Q ss_pred HHHHHHHHHhcCCCCCHHHHHH-HHHHhhhCCCCchhhhhhhccCCCC----HH--HHHHhhccccccCCCCHHHHHHHH
Q 027312 144 FDKGLLYAKTHSHFTNPQAVKG-LFQSLSEHGVTDGEICVIANICPET----VE--EAYAIVPSLKAKRSRLNDLLKEVL 216 (225)
Q Consensus 144 f~KTleYl~rFSk~k~~esv~~-VrelL~~~~L~kfEiAqLaNL~PeT----~e--EAkaLIPSLk~K~~~~de~Lq~IL 216 (225)
..+++-||.+|..+-+++.+.. +.+++.-+.. +.-.+++.-+. .. .++.++|+| -+|++++.++
T Consensus 4 ~~es~tyvDr~gnals~e~v~~aL~ea~R~~~s----~~~~a~~~~~gk~~~~kegk~~~~~~~l-----ptdeeVe~f~ 74 (97)
T TIGR01878 4 YSESPTYVDRFGNALSKEAVEVALYEAQRILRS----IREGADIDIEGKRYMEKEGKNRILVGYL-----PTDKEVEDFL 74 (97)
T ss_pred ccCCchHHHHHHhhcCHHHHHHHHHHHHHHHHH----HHhhhhHHHHhHHHhhhcCcceeecCCC-----CcHHHHHHHH
Confidence 4567889999998778776654 3444442211 01122222111 11 234667754 3799999999
Q ss_pred HHHH
Q 027312 217 IQLA 220 (225)
Q Consensus 217 d~Ls 220 (225)
..+.
T Consensus 75 r~~~ 78 (97)
T TIGR01878 75 RDVR 78 (97)
T ss_pred HHhH
Confidence 8654
No 22
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=32.26 E-value=85 Score=24.61 Aligned_cols=58 Identities=24% Similarity=0.289 Sum_probs=40.1
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCchhhhh-hhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhh
Q 027312 155 SHFTNPQAVKGLFQSLSEHGVTDGEICV-IANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKF 222 (225)
Q Consensus 155 Sk~k~~esv~~VrelL~~~~L~kfEiAq-LaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~ 222 (225)
|.|. .+.-...|+++...|+.-|.+-| +|-+.|+ ||+|+|..- -.|-|+.|=..|.++
T Consensus 31 CGW~-d~ik~mcrniimEkG~~n~tvdqL~AeitPk----aRaLVPd~V-----KkEll~rirt~L~~~ 89 (92)
T KOG4479|consen 31 CGWH-DDIKEMCRNIIMEKGVDNITVDQLAAEITPK----ARALVPDVV-----KKELLLRIRTALDKH 89 (92)
T ss_pred cccH-HHHHHHHHHHHHHhccccccHHHHHHHhCch----hhhhchHHH-----HHHHHHHHHHHHHHH
Confidence 4443 34555678888888998888887 5677785 899999532 356677666666543
No 23
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=31.96 E-value=2.3e+02 Score=21.59 Aligned_cols=77 Identities=12% Similarity=0.152 Sum_probs=53.0
Q ss_pred CCCchHHHHHHHHHHHhcCCCCCHHHHHH----HHHHhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHH
Q 027312 137 TIKIPVSFDKGLLYAKTHSHFTNPQAVKG----LFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLL 212 (225)
Q Consensus 137 ~~~~s~Vf~KTleYl~rFSk~k~~esv~~----VrelL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~L 212 (225)
..++...-.+-.+|+..+..-...-+-+. +++.-...++++.+.....+++-++.+|. .++++.+
T Consensus 35 ~~d~~~~~~~~~~fl~~~~GGp~~Y~~~~G~p~m~~~H~~l~it~~~f~~~~~~~~~al~~~-----------~v~~~~~ 103 (120)
T PF01152_consen 35 GIDLEKHKEKQAEFLSQLLGGPPLYTGRDGHPMMREAHAHLGITEEHFDRWLELLKQALDEL-----------GVPEELI 103 (120)
T ss_dssp TSCHHHHHHHHHHHHHHHTTSSSHHHHHHSSH-HHHHHTTS-BBHHHHHHHHHHHHHHHHHT-----------TCTHHHH
T ss_pred CCCHHHHHHHHHHHHHHHhCCCCCCcccCCCchHHHHHhCCCCCHHHHHHHHHHHHHHHHHh-----------CCCHHHH
Confidence 34566677888889988766655555455 77777777888777666665555554442 2578889
Q ss_pred HHHHHHHHhhhc
Q 027312 213 KEVLIQLAKFKS 224 (225)
Q Consensus 213 q~ILd~Lsk~r~ 224 (225)
++++..+..+|.
T Consensus 104 ~~~~~~~~~~~~ 115 (120)
T PF01152_consen 104 DELLARLESLRD 115 (120)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 999999888874
No 24
>CHL00181 cbbX CbbX; Provisional
Probab=31.41 E-value=2e+02 Score=26.11 Aligned_cols=54 Identities=15% Similarity=0.035 Sum_probs=33.1
Q ss_pred cccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 027312 112 CLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLS 171 (225)
Q Consensus 112 cLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~ 171 (225)
.++..|...|++....+.. ... .......-++|+.+-......-.++.||+++.
T Consensus 195 ~~t~~el~~I~~~~l~~~~-----~~l-~~~~~~~L~~~i~~~~~~~~~GNaR~vrn~ve 248 (287)
T CHL00181 195 DYTPEELLQIAKIMLEEQQ-----YQL-TPEAEKALLDYIKKRMEQPLFANARSVRNALD 248 (287)
T ss_pred CcCHHHHHHHHHHHHHHhc-----CCC-ChhHHHHHHHHHHHhCCCCCCccHHHHHHHHH
Confidence 6778899999887765431 111 11335666788877554444455667776665
No 25
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=31.26 E-value=2.1e+02 Score=21.39 Aligned_cols=59 Identities=15% Similarity=0.098 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCC-CCchhhhhhhccCCCCHH---HHHHhhccccc
Q 027312 143 SFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHG-VTDGEICVIANICPETVE---EAYAIVPSLKA 203 (225)
Q Consensus 143 Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~-L~kfEiAqLaNL~PeT~e---EAkaLIPSLk~ 203 (225)
.|++-++-+++++-= .+....+..++.... ++-.++++|.+++.-+-+ =++.|.|.+-+
T Consensus 9 ~f~~~~~~lk~~~fd--~dkl~~l~~~~~~~~~~T~~Qv~~il~~f~fd~~kl~~lk~l~p~i~D 71 (95)
T PF14771_consen 9 DFEQFLEQLKKESFD--SDKLKVLEAAAKTNNCFTCAQVKQILSLFSFDNDKLKALKLLYPYIVD 71 (95)
T ss_pred HHHHHHHHHHcCCCc--HHHHHHHHHHHhcCCceeHHHHHHHHHHcCCCHHHHHHHHHHhhhccC
Confidence 355555555555322 344555555555545 777777777777777643 34555665544
No 26
>KOG4204 consensus Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics]
Probab=30.42 E-value=4e+02 Score=23.87 Aligned_cols=104 Identities=20% Similarity=0.263 Sum_probs=69.3
Q ss_pred ccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcC--CCCCHHHHHHHHHHhhhC-----CCCc-----hhh
Q 027312 113 LMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHS--HFTNPQAVKGLFQSLSEH-----GVTD-----GEI 180 (225)
Q Consensus 113 LsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFS--k~k~~esv~~VrelL~~~-----~L~k-----fEi 180 (225)
++...|.-.|+.++++.. + .+++++.-++=++.|. ++..++.+..|.++|+.+ |+.. +.+
T Consensus 17 ~t~~DAlsYl~~VK~~f~----d----~p~kY~~FL~im~d~ka~~iD~~~vi~rv~eLfK~h~~Ll~gfN~fLP~~~~i 88 (231)
T KOG4204|consen 17 LTLDDALAYLKAVKEAFQ----D----EPEKYDEFLEIMKDFKAQRIDTPGVIARVKELLKGHPDLLLGFNTFLPPGYKI 88 (231)
T ss_pred CChHHHHHHHHHHHHHHh----c----ChHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHccCHHHHHHHHhhCccccee
Confidence 888999999999988752 1 2356777777666643 577789999999999732 1110 111
Q ss_pred hhhh---------------c-------------cCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHhhhc
Q 027312 181 CVIA---------------N-------------ICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKS 224 (225)
Q Consensus 181 AqLa---------------N-------------L~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~ 224 (225)
.... . +-+-+.++|...|--|+.++.-+++..+.+|++|..|++
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~fv~klk~rf~~~~~v~~s~l~il~~y~~ 160 (231)
T KOG4204|consen 89 TLSSEAKDEFTIYGATSYLPSPKVAFHEEILKLLEDVEFDRAISFVNKLKTRFQGDDHVYKSFLEILRMYQE 160 (231)
T ss_pred ccCcccccccccccccccCCCccccccchhhhhcccchHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhh
Confidence 1000 0 000345678888877888866677889999999998864
No 27
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=29.96 E-value=29 Score=28.81 Aligned_cols=44 Identities=20% Similarity=0.234 Sum_probs=32.6
Q ss_pred Cchh-hhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHH
Q 027312 176 TDGE-ICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQL 219 (225)
Q Consensus 176 ~kfE-iAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~L 219 (225)
..+. .-.++||.|++++++-.-.-+|+.=...+|++|..||+..
T Consensus 67 P~l~~WL~vVgl~~~~i~~i~~~~~tLe~Llemsd~el~~~l~~~ 111 (129)
T PF13543_consen 67 PSLRQWLRVVGLRPESIQAILSKVLTLEALLEMSDEELKEILNRC 111 (129)
T ss_pred CcHHHHhhhcCCCHHHHHHHHHhhcCHHHHHhCCHHHHHHHHHHh
Confidence 3444 5569999999999986555566664457999999998764
No 28
>cd08325 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5),
Probab=28.80 E-value=96 Score=23.24 Aligned_cols=58 Identities=17% Similarity=0.223 Sum_probs=39.8
Q ss_pred HHHHHHH-HHhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHh
Q 027312 161 QAVKGLF-QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAK 221 (225)
Q Consensus 161 esv~~Vr-elL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk 221 (225)
..+..|. .+|...-|++.|+..|--=-+...|-|+.||-++.+| .+...+-.++.|.+
T Consensus 16 ~~i~~llD~Ll~~~Vl~~~E~e~i~~~~~t~~dkar~Lid~v~~K---G~~A~~iF~~~L~~ 74 (83)
T cd08325 16 GVINGLLDDLLEKNVLNEEEMEKIKEENNTIMDKARVLVDSVTEK---GQEAGQIFIKHLLN 74 (83)
T ss_pred hhHHHHHHHHHHcCCCCHHHHHHHHhccCCHHHHHHHHHHHHHHH---hHHHHHHHHHHHHh
Confidence 3444444 3444456888888776655566799999999999987 56666666666654
No 29
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=28.34 E-value=43 Score=24.27 Aligned_cols=33 Identities=24% Similarity=0.372 Sum_probs=15.8
Q ss_pred CCCHHHHHHhhccccccC-------CCCHHHHHHHHHHHH
Q 027312 188 PETVEEAYAIVPSLKAKR-------SRLNDLLKEVLIQLA 220 (225)
Q Consensus 188 PeT~eEAkaLIPSLk~K~-------~~~de~Lq~ILd~Ls 220 (225)
|.+.+||+.++..|.+.. .+++++.+.|+|.|+
T Consensus 6 p~~~~D~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~ 45 (73)
T PF04472_consen 6 PKSFEDAREIVDALREGKIVIVNLENLDDEEAQRILDFLS 45 (73)
T ss_dssp -SSGGGHHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHH
T ss_pred eCCHHHHHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHh
Confidence 444444444444444431 345566666666665
No 30
>COG4003 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.46 E-value=45 Score=26.35 Aligned_cols=25 Identities=24% Similarity=0.275 Sum_probs=12.2
Q ss_pred CCCHHHHHHhhccccccCCCCHHHH
Q 027312 188 PETVEEAYAIVPSLKAKRSRLNDLL 212 (225)
Q Consensus 188 PeT~eEAkaLIPSLk~K~~~~de~L 212 (225)
|+|.|||-.+|.-|+.+..++++..
T Consensus 44 CdT~EEAlEii~yleKrGEi~~E~A 68 (98)
T COG4003 44 CDTEEEALEIINYLEKRGEITPEMA 68 (98)
T ss_pred hCcHHHHHHHHHHHHHhCCCCHHHH
Confidence 4455555555555544444444443
No 31
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, 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 DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=27.38 E-value=1.7e+02 Score=20.65 Aligned_cols=54 Identities=17% Similarity=0.168 Sum_probs=37.8
Q ss_pred HHHHHHhh-hCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHh
Q 027312 164 KGLFQSLS-EHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAK 221 (225)
Q Consensus 164 ~~VrelL~-~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk 221 (225)
..|...|. +.-|+..|...|-. +|...+-++.||-.|..| .++.....++.|..
T Consensus 16 ~~il~~L~~~~vlt~~e~~~i~~-~~~~~~k~~~Lld~l~~k---g~~af~~F~~~L~~ 70 (80)
T cd01671 16 EDVLDHLLSDGVLTEEEYEKIRS-ESTRQDKARKLLDILPRK---GPKAFQSFLQALQE 70 (80)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHc-CCChHHHHHHHHHHHHhc---ChHHHHHHHHHHHh
Confidence 33444443 33466666555544 677899999999999987 78888888888864
No 32
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=26.92 E-value=94 Score=26.19 Aligned_cols=42 Identities=19% Similarity=0.278 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCC-CCchhhhhh
Q 027312 142 VSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHG-VTDGEICVI 183 (225)
Q Consensus 142 ~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~-L~kfEiAqL 183 (225)
.+|.+.++|+-.-..+.-.+.+..|.+.-.+++ +-..|+|.+
T Consensus 85 ~~fe~ild~ia~~~g~~~~evv~~in~~q~~~~~~l~~e~aal 127 (144)
T PF09999_consen 85 DPFERILDYIAAKTGIEKQEVVAEINELQEELGGLLDPEAAAL 127 (144)
T ss_pred cHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCCHHHHHH
Confidence 579999999999888888899999999777776 557776653
No 33
>KOG2759 consensus Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion]
Probab=25.82 E-value=64 Score=31.94 Aligned_cols=47 Identities=17% Similarity=0.162 Sum_probs=30.7
Q ss_pred CCCCchhhhhhhccCCCCH-HHHHH-------------hhccccccCCCCHHHHHHHHHHHH
Q 027312 173 HGVTDGEICVIANICPETV-EEAYA-------------IVPSLKAKRSRLNDLLKEVLIQLA 220 (225)
Q Consensus 173 ~~L~kfEiAqLaNL~PeT~-eEAka-------------LIPSLk~K~~~~de~Lq~ILd~Ls 220 (225)
.++...=++.+.||||... -|.+- .+-+|+.| .++||+|-+-++-|.
T Consensus 256 EKV~Rivlai~~Nll~k~~~~~~~k~~~~~mv~~~v~k~l~~L~~r-kysDEDL~~di~~L~ 316 (442)
T KOG2759|consen 256 EKVTRIVLAIFRNLLDKGPDRETKKDIASQMVLCKVLKTLQSLEER-KYSDEDLVDDIEFLT 316 (442)
T ss_pred HHHHHHHHHHHHHHhccCchhhHHHHHHHHHHhcCchHHHHHHHhc-CCCcHHHHHHHHHHH
Confidence 3566666778999999873 22222 23566664 599998877666655
No 34
>PF05635 23S_rRNA_IVP: 23S rRNA-intervening sequence protein; InterPro: IPR008815 This family consists of bacterial proteins encoded within an intervening sequence present within some 23S rRNA genes[]. The function of these proteins is not known, but a structural study indicates that each momonmer folds into an antiparallel four-helix bundle, while the overall protein is a homopentamer with a toroid-shaped structure containing a tapered central channel [].; PDB: 2GSC_E 2RLD_D.
Probab=24.80 E-value=1.1e+02 Score=23.41 Aligned_cols=80 Identities=6% Similarity=-0.051 Sum_probs=53.4
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhh---------hCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHH
Q 027312 144 FDKGLLYAKTHSHFTNPQAVKGLFQSLS---------EHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKE 214 (225)
Q Consensus 144 f~KTleYl~rFSk~k~~esv~~VrelL~---------~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ 214 (225)
....+.-++.|.++....-..++++.-. ....++-+..+..++.=..+.|.+..+--+.+..-+++++.+.
T Consensus 16 ~~~i~~~~~~~p~~e~~~l~~Qi~raa~SI~~NIaEg~~r~s~~d~~~~l~iA~~s~~E~~~~L~~a~~~~~i~~~~~~~ 95 (110)
T PF05635_consen 16 ALEIYELTKSFPKEEKFSLRDQIRRAATSIPANIAEGNGRRSKKDFIRFLYIARGSLAELRYWLELARDLGYISEEEYEE 95 (110)
T ss_dssp HHHHHHHHCCCHCCGTTTHHHHHHHHHHHHHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHH
T ss_pred HHHHHHHHHhCcHhhhhhHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence 3344555566766666556666664332 1246777888877888888999999997766655578888777
Q ss_pred HHHHHHhhh
Q 027312 215 VLIQLAKFK 223 (225)
Q Consensus 215 ILd~Lsk~r 223 (225)
+...+..+.
T Consensus 96 l~~~~~ei~ 104 (110)
T PF05635_consen 96 LKKELEEIS 104 (110)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 777666554
No 35
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=24.76 E-value=73 Score=21.68 Aligned_cols=17 Identities=12% Similarity=0.192 Sum_probs=13.5
Q ss_pred CCHHHHHHHHHHHHhhh
Q 027312 207 RLNDLLKEVLIQLAKFK 223 (225)
Q Consensus 207 ~~de~Lq~ILd~Lsk~r 223 (225)
++++|++.|+.-|.+++
T Consensus 75 ls~~e~~~l~ayl~slk 91 (91)
T PF00034_consen 75 LSDEEIADLAAYLRSLK 91 (91)
T ss_dssp SSHHHHHHHHHHHHHTS
T ss_pred CCHHHHHHHHHHHHHhC
Confidence 78888888888887764
No 36
>PRK07168 bifunctional uroporphyrinogen-III methyltransferase/uroporphyrinogen-III synthase; Reviewed
Probab=24.22 E-value=75 Score=31.27 Aligned_cols=58 Identities=16% Similarity=0.186 Sum_probs=47.0
Q ss_pred CCCCHHHHHHHHHHhhhCCCCchhhhhhhccCCCCHHHHHHh-hccccccCCCCHHHHHHHHHHHH
Q 027312 156 HFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAI-VPSLKAKRSRLNDLLKEVLIQLA 220 (225)
Q Consensus 156 k~k~~esv~~VrelL~~~~L~kfEiAqLaNL~PeT~eEAkaL-IPSLk~K~~~~de~Lq~ILd~Ls 220 (225)
-|.++.+|+.+.+.++..++.+...+.++.+-|-|.+.|+.. +- --|.++|++|+.=.
T Consensus 412 iFtS~ssV~~f~~~~~~~~~~~~~~~~~~~iGp~t~~~a~~~G~~-------~~~~~~~~~~~~~~ 470 (474)
T PRK07168 412 VFEGRASIDTFLAEVKRLGFIDIVTLPFSYTDVPTLHYANKVGFH-------NIDHQLQETLMQKD 470 (474)
T ss_pred EECCHHHHHHHHHHHHhhCchhhccCceEEeCHHHHHHHHHhCCC-------cccHHHHHHHhhhh
Confidence 588999999999999988887776666889999999999875 33 35788999987643
No 37
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=24.02 E-value=58 Score=24.43 Aligned_cols=79 Identities=14% Similarity=0.168 Sum_probs=42.9
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchh-hhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHh
Q 027312 143 SFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGE-ICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAK 221 (225)
Q Consensus 143 Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfE-iAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk 221 (225)
.+-|+-.||.++-++-+ .=..|++++....+.... +..|..++-+..++++.+|-.-.. ..++...++.+.+.|..
T Consensus 12 ~lGks~s~Vs~~l~Ll~--lP~~i~~~v~~g~~~~~~a~~~L~~~~~~~~~~~~~~v~~~~~-~~~t~~~~~~~~~~l~~ 88 (93)
T PF08535_consen 12 RLGKSRSWVSNHLALLD--LPEEIKELVRSGRISDIRALYELRKLAEKNPEEVEALVAKAKE-EGLTRAAVKALRRELKE 88 (93)
T ss_dssp HTT--HHHHHHHHGGGS----HHHHHHHHTTS---HHHHHHHHHHHHH-HHHHHHHH-HSTT-S--SHHHHHHHHHHHH-
T ss_pred HHCCCHHHHHHHHHHHc--CCHHHHHHHHcCCCchHHHHHHHHHHHHhCHHHHHHHHHHhcc-ccccHHHHHHHHHHHHH
Confidence 34456667766666543 233466677765566655 334777777889999999922112 24788999999888876
Q ss_pred hhc
Q 027312 222 FKS 224 (225)
Q Consensus 222 ~r~ 224 (225)
-++
T Consensus 89 ~k~ 91 (93)
T PF08535_consen 89 KKR 91 (93)
T ss_dssp ---
T ss_pred hhc
Confidence 543
No 38
>PF14762 HPS3_Mid: Hermansky-Pudlak syndrome 3, middle region
Probab=23.13 E-value=2.6e+02 Score=27.09 Aligned_cols=108 Identities=11% Similarity=0.058 Sum_probs=59.0
Q ss_pred cHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHh-cCCCCCHHHHHHHHHHhhhCCCCchhhhhhhccCCCCHH
Q 027312 114 MDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKT-HSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVE 192 (225)
Q Consensus 114 snsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~r-FSk~k~~esv~~VrelL~~~~L~kfEiAqLaNL~PeT~e 192 (225)
-++|++.||+...-+..+.......++...|+..-.++-. |++.. .+......-..+..++.-.|+..-+++.-.++.
T Consensus 252 LL~EaHlLLRsaL~~~~~~~~~~~~eL~~l~reSca~LGD~~~r~~-~~d~~lA~pYYkMS~l~i~~Vl~ri~~~~~~~~ 330 (374)
T PF14762_consen 252 LLSEAHLLLRSALLDPSQEESEEKNELRELFRESCALLGDCYSRSD-EKDYHLAAPYYKMSGLSISEVLNRIKLVKSDVS 330 (374)
T ss_pred HHHHHHHHHHHHhhhhhhcccchHHHHHHHHHHHHHHHHhHhhccc-hHHHHHHHHHHHhcCCCHHHHHHHhhhcccccc
Confidence 4689999998776222222223334566788888888877 77765 333333334445556766665554444322111
Q ss_pred H---HHHhhcccccc------CCCCHHHHHHHHHHHHhh
Q 027312 193 E---AYAIVPSLKAK------RSRLNDLLKEVLIQLAKF 222 (225)
Q Consensus 193 E---AkaLIPSLk~K------~~~~de~Lq~ILd~Lsk~ 222 (225)
+ .+.||=-|+.. -..+++-.++||++....
T Consensus 331 ~~~~~~GLi~yLk~~L~~~~~~~lseela~~il~i~~~~ 369 (374)
T PF14762_consen 331 QSYDGRGLIFYLKHVLYEEESEELSEELANKILQIFSQA 369 (374)
T ss_pred cccccchHHHHHHHHhccccchhhhHHHHHHHHHHHHhc
Confidence 1 33444333221 135666677777776543
No 39
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. 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 CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=22.41 E-value=3.5e+02 Score=20.86 Aligned_cols=75 Identities=13% Similarity=0.112 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHHHh
Q 027312 142 VSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQLAK 221 (225)
Q Consensus 142 ~Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk 221 (225)
+.+++.++|+-.--. ....+.+....||++-+|-.|-.=-|.+.|-.+.++-.-..+ .=....++.+++.|..
T Consensus 4 ~~l~~~f~~i~~~V~------~~~Wk~laR~LGLse~~I~~i~~~~~~~~eq~~qmL~~W~~~-~G~~At~~~L~~aL~~ 76 (96)
T cd08315 4 ETLRRSFDHFIKEVP------FDSWNRLMRQLGLSENEIDVAKANERVTREQLYQMLLTWVNK-TGRKASVNTLLDALEA 76 (96)
T ss_pred hHHHHHHHHHHHHCC------HHHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHh-hCCCcHHHHHHHHHHH
Confidence 557777777753221 234666777789999998887777788866666666544433 2245667888877776
Q ss_pred hh
Q 027312 222 FK 223 (225)
Q Consensus 222 ~r 223 (225)
+.
T Consensus 77 ~~ 78 (96)
T cd08315 77 IG 78 (96)
T ss_pred cc
Confidence 53
No 40
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=22.15 E-value=54 Score=22.18 Aligned_cols=30 Identities=10% Similarity=0.087 Sum_probs=15.2
Q ss_pred CCCCHHHHHHhhccccccCCCCHHHHHHHH
Q 027312 187 CPETVEEAYAIVPSLKAKRSRLNDLLKEVL 216 (225)
Q Consensus 187 ~PeT~eEAkaLIPSLk~K~~~~de~Lq~IL 216 (225)
+.....+...|+|-|..-..|++++.+.|+
T Consensus 17 ~~~~~~~~~~llpvi~tlL~fs~~e~~~i~ 46 (46)
T PF01465_consen 17 ESREPSEREQLLPVIATLLKFSPEEKQKIL 46 (46)
T ss_dssp TTSS---HHHHHHHHHHHTT--HHHHHHHH
T ss_pred cCCchhhHHHHHHHHHHHHCCCHHHHHhhC
Confidence 334456666677766665457777777664
No 41
>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX. Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.
Probab=22.14 E-value=3e+02 Score=24.78 Aligned_cols=55 Identities=5% Similarity=-0.043 Sum_probs=37.1
Q ss_pred cccHHHHHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhh
Q 027312 112 CLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSE 172 (225)
Q Consensus 112 cLsnsEV~~ILe~~~e~~~~~s~d~~~~~s~Vf~KTleYl~rFSk~k~~esv~~VrelL~~ 172 (225)
.|+..|...|++....+. ..... ...+....+|+........+-+++.+|+++.+
T Consensus 194 ~l~~edl~~I~~~~l~~~-----~~~l~-~~a~~~L~~~l~~~~~~~~~GN~R~lrn~ve~ 248 (284)
T TIGR02880 194 DYSEAELLVIAGLMLKEQ-----QYRFS-AEAEEAFADYIALRRTQPHFANARSIRNAIDR 248 (284)
T ss_pred CcCHHHHHHHHHHHHHHh-----ccccC-HHHHHHHHHHHHHhCCCCCCChHHHHHHHHHH
Confidence 677899999988876553 11111 24455666788776666667888888888764
No 42
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=21.92 E-value=83 Score=28.26 Aligned_cols=33 Identities=24% Similarity=0.248 Sum_probs=26.3
Q ss_pred HHHHHHhhhCCCCchhhhh---hhccCCCCHHHHHH
Q 027312 164 KGLFQSLSEHGVTDGEICV---IANICPETVEEAYA 196 (225)
Q Consensus 164 ~~VrelL~~~~L~kfEiAq---LaNL~PeT~eEAka 196 (225)
..+.+.|+.+||++.|+-. |.+++|-|+-|+-.
T Consensus 3 ~~~~~~L~~lGlt~yEa~vY~aLl~~g~~tA~eis~ 38 (247)
T COG1378 3 EELEENLQKLGLTEYEAKVYLALLCLGEATAKEISE 38 (247)
T ss_pred hHHHHHHHHcCCCHHHHHHHHHHHHhCCccHHHHHH
Confidence 3577889999999999544 77888999988643
No 43
>PF09524 Phg_2220_C: Conserved phage C-terminus (Phg_2220_C); InterPro: IPR011741 This entry is represented by the C-terminal domain of Bacteriophage r1t, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=21.75 E-value=1.5e+02 Score=22.24 Aligned_cols=51 Identities=22% Similarity=0.206 Sum_probs=29.2
Q ss_pred HHHHHh--cCCCC--CHHHHHHHHHHhhhCCCCchhhhh-hhccCCC---CHHHHHHhhc
Q 027312 148 LLYAKT--HSHFT--NPQAVKGLFQSLSEHGVTDGEICV-IANICPE---TVEEAYAIVP 199 (225)
Q Consensus 148 leYl~r--FSk~k--~~esv~~VrelL~~~~L~kfEiAq-LaNL~Pe---T~eEAkaLIP 199 (225)
++|+++ -++|+ +..+.+.|+..|.. |.+..+... |-+.|-+ |..-++.|=|
T Consensus 2 I~yLN~~tg~~f~~~~~~~~~~I~aRl~e-G~t~edf~~VID~k~~~W~~~~~m~~YLRP 60 (74)
T PF09524_consen 2 IDYLNKKTGKKFKSNTKSTKKLIKARLNE-GYTLEDFKKVIDNKVAEWKGDPKMEKYLRP 60 (74)
T ss_pred HHHHHHHhcCccCCCcHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHCCCHHHHHhcCc
Confidence 567777 45666 46667777777765 776666443 3333322 3445555555
No 44
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.43 E-value=2.1e+02 Score=22.05 Aligned_cols=40 Identities=18% Similarity=0.197 Sum_probs=24.6
Q ss_pred HHHHHHHHH--HhhhCCCCchhhhhhhccCC---CCHHHHHHhhc
Q 027312 160 PQAVKGLFQ--SLSEHGVTDGEICVIANICP---ETVEEAYAIVP 199 (225)
Q Consensus 160 ~esv~~Vre--lL~~~~L~kfEiAqLaNL~P---eT~eEAkaLIP 199 (225)
++.+..++. .|...||+=.||..+.+.++ .++++...++-
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~ 85 (113)
T cd01109 41 EEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPERLELLE 85 (113)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHccCCccHHHHHHHHH
Confidence 455555543 34567898888888777654 34556665554
No 45
>COG3310 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.17 E-value=1.3e+02 Score=26.47 Aligned_cols=44 Identities=30% Similarity=0.440 Sum_probs=27.7
Q ss_pred hhhhhhh-ccCCCCH-----HHHHHhhccccccCCCCHHHHHHHHHHHHhhhcC
Q 027312 178 GEICVIA-NICPETV-----EEAYAIVPSLKAKRSRLNDLLKEVLIQLAKFKST 225 (225)
Q Consensus 178 fEiAqLa-NL~PeT~-----eEAkaLIPSLk~K~~~~de~Lq~ILd~Lsk~r~~ 225 (225)
.|.|+|+ ||||--. .-+|. .-| +. +..+.-|+.|-++|..+|.|
T Consensus 23 le~aVIGLNLCPFAka~~vkqqvri-~vS-eA--~~~e~lLehl~~ell~L~~t 72 (196)
T COG3310 23 LEKAVIGLNLCPFAKAPHVKQQVRI-AVS-EA--THLEALLEHLDEELLRLRNT 72 (196)
T ss_pred HHHHHHhhccCccccchhhhhhhhe-eee-cc--cChHHHHHHHHHHHHHhcCC
Confidence 3556665 9999741 22222 233 23 36778888898888888865
No 46
>PRK09726 antitoxin HipB; Provisional
Probab=20.97 E-value=2.2e+02 Score=21.05 Aligned_cols=53 Identities=15% Similarity=0.108 Sum_probs=34.2
Q ss_pred HHHHHHHHHhhhCCCCchhhhhhhccCCCCHHHHHHhhccccccCCCCHHHHHHHHHHH
Q 027312 161 QAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLNDLLKEVLIQL 219 (225)
Q Consensus 161 esv~~VrelL~~~~L~kfEiAqLaNL~PeT~eEAkaLIPSLk~K~~~~de~Lq~ILd~L 219 (225)
.-...|+++....+++..|.|..+++-+.++-.... .+...+-+.|..|++.+
T Consensus 12 ~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~------g~~~ps~~~l~~ia~~l 64 (88)
T PRK09726 12 QLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN------NPDNTTLTTFFKILQSL 64 (88)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC------CCCCCCHHHHHHHHHHc
Confidence 344566677777899999999999888777643322 11134566666666544
No 47
>PF09702 Cas_Csa5: CRISPR-associated protein (Cas_Csa5); InterPro: IPR010157 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a minor family of Cas protein found in various species of Sulfolobus and Pyrococcus (all archaeal). It is found with two different CRISPR loci in Sulfolobus solfataricus.
Probab=20.82 E-value=39 Score=27.29 Aligned_cols=73 Identities=18% Similarity=0.238 Sum_probs=41.5
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHH-HHhhh--CCCCchhhhh----hhccCCC----CHHHHHHhhccccccCCCCHHHH
Q 027312 144 FDKGLLYAKTHSHFTNPQAVKGLF-QSLSE--HGVTDGEICV----IANICPE----TVEEAYAIVPSLKAKRSRLNDLL 212 (225)
Q Consensus 144 f~KTleYl~rFSk~k~~esv~~Vr-elL~~--~~L~kfEiAq----LaNL~Pe----T~eEAkaLIPSLk~K~~~~de~L 212 (225)
..+...|++||+.--++|.+..+. +.|.- .++..-|+-. =.+..|. .-|--+.++|+|- +++++
T Consensus 4 ~~e~~~~vDRiaNALs~E~v~~aL~dAlR~~~s~~~s~ei~~~~~~~~~~y~~v~~~ekeg~~i~~g~lP-----t~~eV 78 (105)
T PF09702_consen 4 YTESFTYVDRIANALSPEAVEVALYDALRIFRSIIDSAEIDKSQVEEGRRYIAVIVKEKEGNYIIVGYLP-----TDEEV 78 (105)
T ss_pred eecCccHHHHHHhhcCHHHHHHHHHHHHHHHHHHhccccccccccccCccccceeeccCCCCEEecCCCC-----ChHHH
Confidence 456778999999988888665433 44431 1222212111 1233331 2222345667654 79999
Q ss_pred HHHHHHHHh
Q 027312 213 KEVLIQLAK 221 (225)
Q Consensus 213 q~ILd~Lsk 221 (225)
+..|+.+.+
T Consensus 79 e~Fl~~v~~ 87 (105)
T PF09702_consen 79 EDFLDDVER 87 (105)
T ss_pred HHHHHHHHH
Confidence 999998864
No 48
>TIGR02498 type_III_ssaH type III secretion system protein, SsaH family. This family describes a small protein, always smaller than 100 amino acids, encoded in pathogenicity islands for bacterial type III secretion systems in various strains of Yersinia, Salmonella, and enteropathogenic E. coli, as well as Chromobacterium violaceum and Citrobacter rodentium. Although strictly associated with type III secretion systems, this protein seems not yet to have been characterized as part of the apparatus or as an effector protein.
Probab=20.80 E-value=2.4e+02 Score=21.78 Aligned_cols=57 Identities=9% Similarity=0.053 Sum_probs=43.4
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHhhhCCCCchhhhh--hhccCCCCHHHHHHhhc
Q 027312 143 SFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICV--IANICPETVEEAYAIVP 199 (225)
Q Consensus 143 Vf~KTleYl~rFSk~k~~esv~~VrelL~~~~L~kfEiAq--LaNL~PeT~eEAkaLIP 199 (225)
+...+..-++-|-.+-....++.+-+.+-.+||.+-+.|. |++.-+++++-.|+|++
T Consensus 21 L~~ea~ailnalP~li~D~~~r~vcea~llfGL~~~~~A~~~L~~~~~~eA~~Lr~l~~ 79 (79)
T TIGR02498 21 LPKEAHSILNALPQIIPDKKDRLVCEAILLFGLNHKNDAVKLLENMDDEEAQLLRSLVN 79 (79)
T ss_pred cHHHHHHHHHhcccccCCHhHHHHHHHHHHHhcCcHHHHHHHHhcCCcHHHHHHHHHhC
Confidence 4667777788888877777788888888889999888554 88877777766666653
Done!