Query 013256
Match_columns 447
No_of_seqs 128 out of 286
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 02:00:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013256.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013256hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2636 Splicing factor 3a, su 100.0 1E-120 3E-125 918.0 34.1 421 3-443 1-429 (497)
2 COG5188 PRP9 Splicing factor 3 100.0 3.7E-87 8E-92 657.8 27.0 378 4-440 2-399 (470)
3 PF11931 DUF3449: Domain of un 100.0 3.6E-53 7.7E-58 396.2 6.0 112 329-440 1-126 (196)
4 PF13297 Telomere_Sde2_2: Telo 99.6 9.7E-16 2.1E-20 117.3 4.9 59 247-305 2-60 (60)
5 PF12108 SF3a60_bindingd: Spli 98.9 6.9E-10 1.5E-14 73.0 2.7 23 84-106 6-28 (28)
6 KOG2827 Uncharacterized conser 98.5 6.5E-08 1.4E-12 95.0 4.6 61 245-305 261-321 (322)
7 PF12171 zf-C2H2_jaz: Zinc-fin 94.6 0.0056 1.2E-07 39.7 -1.1 26 249-280 2-27 (27)
8 PF12874 zf-met: Zinc-finger o 90.3 0.14 3.1E-06 32.0 1.1 21 416-437 1-21 (25)
9 PF12874 zf-met: Zinc-finger o 88.0 0.039 8.5E-07 34.7 -2.8 25 249-279 1-25 (25)
10 smart00451 ZnF_U1 U1-like zinc 87.6 0.11 2.3E-06 35.2 -0.9 29 249-283 4-32 (35)
11 PF06397 Desulfoferrod_N: Desu 86.3 0.21 4.5E-06 35.1 -0.1 13 413-425 4-16 (36)
12 KOG4727 U1-like Zn-finger prot 83.6 3.3 7.2E-05 38.8 6.4 33 245-283 72-104 (193)
13 PF09943 DUF2175: Uncharacteri 79.1 0.89 1.9E-05 39.1 0.9 16 414-429 1-16 (101)
14 COG4481 Uncharacterized protei 79.0 1.1 2.5E-05 34.2 1.4 32 405-436 24-55 (60)
15 PF00096 zf-C2H2: Zinc finger, 78.1 1.1 2.4E-05 27.3 1.0 21 416-437 1-21 (23)
16 TIGR00319 desulf_FeS4 desulfof 77.7 0.82 1.8E-05 31.2 0.3 13 413-425 5-17 (34)
17 KOG2636 Splicing factor 3a, su 77.3 1.2 2.6E-05 47.4 1.5 86 176-282 214-299 (497)
18 PF13894 zf-C2H2_4: C2H2-type 76.9 1.6 3.5E-05 26.2 1.4 21 416-437 1-21 (24)
19 smart00355 ZnF_C2H2 zinc finge 76.4 1.5 3.3E-05 26.5 1.2 21 416-437 1-21 (26)
20 KOG3408 U1-like Zn-finger-cont 76.4 1.6 3.5E-05 38.7 1.8 27 249-281 58-84 (129)
21 PF12171 zf-C2H2_jaz: Zinc-fin 75.6 1.2 2.5E-05 28.7 0.6 21 416-437 2-22 (27)
22 cd00974 DSRD Desulforedoxin (D 75.6 1 2.2E-05 30.8 0.3 12 414-425 3-14 (34)
23 PLN02748 tRNA dimethylallyltra 73.6 1.7 3.7E-05 47.0 1.5 26 412-437 415-440 (468)
24 COG5112 UFD2 U1-like Zn-finger 73.4 3.9 8.5E-05 35.5 3.4 30 249-285 56-85 (126)
25 PF06220 zf-U1: U1 zinc finger 58.8 3.7 8E-05 29.0 0.4 33 249-285 4-36 (38)
26 PF13909 zf-H2C2_5: C2H2-type 57.9 6.6 0.00014 24.2 1.4 20 416-437 1-20 (24)
27 cd00729 rubredoxin_SM Rubredox 56.4 4.4 9.5E-05 27.9 0.4 15 415-430 2-16 (34)
28 KOG0717 Molecular chaperone (D 50.7 4.5 9.8E-05 43.4 -0.4 31 249-285 293-323 (508)
29 PF13465 zf-H2C2_2: Zinc-finge 48.3 11 0.00023 24.1 1.2 17 408-424 7-23 (26)
30 PF13913 zf-C2HC_2: zinc-finge 42.7 13 0.00029 23.7 1.0 20 416-437 3-22 (25)
31 PF13912 zf-C2H2_6: C2H2-type 41.4 14 0.0003 23.2 0.9 21 415-436 1-21 (27)
32 cd00350 rubredoxin_like Rubred 40.5 11 0.00024 25.6 0.4 14 416-430 2-15 (33)
33 PF13824 zf-Mss51: Zinc-finger 38.9 21 0.00046 27.5 1.7 28 411-438 10-37 (55)
34 PRK12496 hypothetical protein; 38.5 7 0.00015 36.4 -1.2 26 404-429 125-157 (164)
35 PF14379 Myb_CC_LHEQLE: MYB-CC 35.6 79 0.0017 24.0 4.3 13 6-18 12-24 (51)
36 PF03941 INCENP_ARK-bind: Inne 32.8 15 0.00033 28.1 0.1 8 398-405 14-21 (57)
37 PF07754 DUF1610: Domain of un 30.3 24 0.00053 22.6 0.7 13 411-423 12-24 (24)
38 PF10146 zf-C4H2: Zinc finger- 29.9 1.2E+02 0.0026 29.9 5.8 23 5-27 51-73 (230)
39 COG4105 ComL DNA uptake lipopr 29.7 79 0.0017 31.7 4.5 40 138-177 87-127 (254)
40 PF13319 DUF4090: Protein of u 29.2 25 0.00054 28.9 0.8 12 395-406 13-24 (84)
41 PF06160 EzrA: Septation ring 28.3 4.3E+02 0.0092 29.3 10.4 89 5-104 342-433 (560)
42 PF00301 Rubredoxin: Rubredoxi 27.7 23 0.00049 26.3 0.3 15 415-430 1-15 (47)
43 cd00730 rubredoxin Rubredoxin; 26.8 22 0.00048 26.7 0.1 14 415-429 1-14 (50)
44 PF02132 RecR: RecR protein; 26.7 21 0.00046 25.4 -0.0 10 416-425 18-27 (41)
45 KOG0324 Uncharacterized conser 26.1 22 0.00048 34.5 0.0 20 399-418 126-145 (214)
46 COG4847 Uncharacterized protei 26.0 28 0.00061 29.7 0.6 16 414-429 5-20 (103)
47 PF09388 SpoOE-like: Spo0E lik 25.4 2.6E+02 0.0057 20.1 5.8 42 12-53 2-43 (45)
48 KOG3454 U1 snRNP-specific prot 24.2 31 0.00068 32.2 0.6 32 249-284 4-35 (165)
49 PRK04778 septation ring format 23.9 5.4E+02 0.012 28.5 10.3 90 4-104 345-437 (569)
50 COG3502 Uncharacterized protei 23.9 44 0.00095 29.3 1.4 17 387-403 86-111 (115)
51 PRK13694 hypothetical protein; 23.3 1.9E+02 0.004 24.2 4.8 18 6-23 11-28 (83)
52 PRK06835 DNA replication prote 23.0 2.3E+02 0.005 29.2 6.7 17 412-428 95-111 (329)
53 KOG2476 Uncharacterized conser 22.2 22 0.00048 38.4 -0.9 42 392-433 56-103 (528)
54 TIGR00009 L28 ribosomal protei 22.0 37 0.0008 26.0 0.5 16 416-431 3-18 (56)
55 PF09620 Cas_csx3: CRISPR-asso 22.0 61 0.0013 26.9 1.8 19 389-407 15-40 (80)
56 PF12756 zf-C2H2_2: C2H2 type 21.4 57 0.0012 26.2 1.6 24 415-439 50-73 (100)
57 PHA02768 hypothetical protein; 21.0 33 0.00073 26.4 0.1 20 415-435 5-24 (55)
58 PF10102 DUF2341: Domain of un 20.9 21 0.00045 29.9 -1.2 14 396-409 10-23 (89)
59 PF04194 PDCD2_C: Programmed c 20.4 17 0.00037 33.6 -2.0 31 396-433 78-110 (164)
60 PF01348 Intron_maturas2: Type 20.4 37 0.00081 30.8 0.3 25 397-423 121-145 (146)
61 PF10267 Tmemb_cc2: Predicted 20.3 3.9E+02 0.0085 28.5 7.9 86 5-99 217-305 (395)
62 PF10073 DUF2312: Uncharacteri 20.3 2.4E+02 0.0051 23.1 4.8 19 7-25 4-22 (74)
63 PF06290 PsiB: Plasmid SOS inh 20.1 47 0.001 30.3 0.9 59 349-425 3-61 (143)
64 PF04502 DUF572: Family of unk 20.0 36 0.00078 35.0 0.1 15 416-430 41-55 (324)
65 KOG1074 Transcriptional repres 20.0 41 0.00089 38.9 0.5 18 406-423 624-641 (958)
No 1
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=100.00 E-value=1.4e-120 Score=917.98 Aligned_cols=421 Identities=47% Similarity=0.736 Sum_probs=380.6
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHhhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccchhhHHHHHHccCCCCC
Q 013256 3 STLLEVTRAAHEEVERLERLVVKDLQTEPNSNKDRLVQSHRVRNMIDTITDTTERLIEIYADKDNARKDEIAALGGQTAT 82 (447)
Q Consensus 3 ~~~LE~~R~~hEeiErlE~ai~~~l~~~p~t~k~~l~q~h~i~~~ld~~~~~~~~L~~~y~D~dg~r~~Ei~~l~g~~~~ 82 (447)
+|+||+||++|||+|||+++||++++++|.+.|++|.+.|+|+.|++++.+.+.+|+++|+|+||+|+.||++|+|
T Consensus 1 etlLEt~R~lhEE~ERl~~~ive~~~~~p~~~k~ri~~~hrv~~~~~~~~~ss~~l~~~yedkdg~r~~e~~~l~g---- 76 (497)
T KOG2636|consen 1 ETLLETQRRLHEEMERLENAIVEREQANPPGKKDRINSEHRVRSFLERYRSSSIKLRKLYEDKDGLRKREIAALSG---- 76 (497)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhCCCchHHHHhHHhhHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHhcC----
Confidence 4799999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCchHHHHHHHHHHHHHhhhhCCCCccccCchhhHHh----hhcc----CCCCcccccccCccccchHHHHHHHhcCCCC
Q 013256 83 GTNVFSSFYDRLKEIREYHRRHPSARVAVDASEDYEN----LLKE----EPLVEFSGEEAYGRYLDLHELYNQYINSKFG 154 (447)
Q Consensus 83 ~~~~f~~Fy~rL~~Ike~hr~~p~~~~~~~~~~~~~~----~~~~----~~~~~Fs~EE~yGryLDL~~~y~~ylNl~~~ 154 (447)
+|+|++||++|++|++||+++|+. ++++....+.. ...+ .+.+.|||+|+||||||||++|.+||||+.+
T Consensus 77 -~n~f~EfY~rLk~I~~~hk~~p~e-~~~p~~v~~~~~~e~~~~~~~~~~~l~~Fs~ee~yGrfldL~d~y~kyinl~~~ 154 (497)
T KOG2636|consen 77 -PNDFAEFYKRLKEINEFHKKHPDE-KDEPKSVRFLELYEARLSPEDENEVLVEFSGEEGYGRFLDLHDCYRKYINLKNV 154 (497)
T ss_pred -chhHHHHHHHHHHHhHHHhcCccc-cccchhHHHHHHHHhhcCccccchhhHhhcccccccccccHHHHHHHHhhhhhh
Confidence 799999999999999999999986 33454444433 3333 2457899999999999999999999999999
Q ss_pred CccchhHHHhhhcCCCCCcccccchhhHHHHHHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHhhCCCCCCcccCc
Q 013256 155 KEIEYSAYLDVFSRPHEIPRKLKMTRQYREYIEKLLEYLIYFFQRTEPLQDLDRIFSKVVADFEEQWVTSTLQGWETEGQ 234 (447)
Q Consensus 155 ~~i~Yl~YL~~f~~f~~ip~~~K~~~~Y~~YL~~L~~YL~~F~~R~~PL~d~~~~~~~~~~~Fe~~W~~g~~~gW~~~~~ 234 (447)
.+++|++||.+|++|.+||+ .+++..|+.||+.|.+||.+|+.|++||.|++++++.+.++|+.+|.+|.+|||....+
T Consensus 155 ~r~~Y~~yL~~fd~~~~ip~-~~k~~~Y~~Yi~~L~eYL~~F~~r~~Pl~d~~~ll~~~~~~f~~~~~aG~lpg~~~~et 233 (497)
T KOG2636|consen 155 ERVDYLEYLKNFDQLDDIPK-EKKNREYLNYIEELNEYLVSFIDRTEPLLDLDKLLAKVPKEFERAWAAGTLPGWKYKET 233 (497)
T ss_pred hhhhHHHHHHHHhhhcccch-hhhhHHHHHHHHHHHHHHHHHHHhcccchhhHhHhcchhhHHHHHHHhCCCCCcccccc
Confidence 99999999999999999999 66699999999999999999999999999999999999999999999999999995432
Q ss_pred CCCCCCCCCCccCccccchHHHHHhhchhhhhHHHHhcccCCCCchHHHHHHhhhhcCCCccchhhhhhhccCCCCCCCC
Q 013256 235 ENGHVPAQHSELDLDYYSTVEELMEVGSERLKEELAAKGLKSGGTLQQRAERLFLTKHTPLDKLDKKHFAKGARGKEQNG 314 (447)
Q Consensus 235 ~~~~~~~~~~~~~~~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~K~ra~rLf~~k~~~~e~~~~~~~ak~~~~~~~~~ 314 (447)
..+ ...++...+++++++++||+||++++.+.+++|||+..+||.|+|+|++++++.+++++|++..+.++
T Consensus 234 ~~~------~~~dl~~~~s~Eel~~~g~erlk~al~alglk~gGt~~~ra~rlf~Tk~~~l~~L~~~~~~kn~s~~~--- 304 (497)
T KOG2636|consen 234 FSA------KALDLSGASSVEELYCLGCERLKSALTALGLKCGGTLHERAQRLFSTKSKSLSHLDTKLFAKNPSKKG--- 304 (497)
T ss_pred ccc------cccccchhhHHHHHHhhchhHHHHHHHHHHHhcCCeecHHHHhhhhhcCcchhhhhhhhhccCcccch---
Confidence 221 12678899999999999999999999999999999999999999999999999999999998766541
Q ss_pred CCCcccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCHHHHHHHHHhhhhhhcCCCCchhhhhhcCCCCCC
Q 013256 315 VAPATQEVGNLKDIALMEAKMKKLCDLLSETIERTIQNVQKKQALTYEEMEAEREEQEETQVDTESDDEEQQIYNPLKLP 394 (447)
Q Consensus 315 ~~~~~~~~~~~k~ia~~E~~I~~l~e~L~~~~~~T~~nveRKqa~T~~Ere~E~e~~~~~~~~~e~~dee~~iyNPlnLP 394 (447)
......+.++||+.|++|.+++.+|+++|.+|++||.|||++|+.|++.|.++ +.+..+++++|+++.||||+|||
T Consensus 305 ---~~~~~~~~keia~tEa~v~k~~~iL~eeR~~t~env~rKq~~ta~e~E~E~~e-q~~~~~e~~~de~~~~ynp~~lP 380 (497)
T KOG2636|consen 305 ---HRREKERNKEIARTEALVKKLLAILAEERKATRENVVRKQARTAEEREEEEEE-QSDSDEESDDDEEELIYNPKNLP 380 (497)
T ss_pred ---hhhhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhhhhh-hhccccccccchhhccCCcccCC
Confidence 23345668999999999999999999999999999999999999999877765 33344445566678999999999
Q ss_pred CCCCCCCchhHHHHHhcCCceeeeeeccCcccchhhhHHHhhhhhhhhh
Q 013256 395 MGWDGKPIPYWLYKLHGLGQVFSSLNCYNLLQDLGFLWINVFYEELCLH 443 (447)
Q Consensus 395 LGwDGkPIPyWLYKLhGL~~ey~CEICGN~~Y~Gr~~~~~~f~~~~~~~ 443 (447)
|||||||||||||||||||++|+||||||+||||||+|+|||.||--.|
T Consensus 381 LGwDGkPiPyWLyKLHGL~~ey~CEICGNy~Y~GrkaF~RHF~EwRH~h 429 (497)
T KOG2636|consen 381 LGWDGKPIPYWLYKLHGLDIEYNCEICGNYVYKGRKAFDRHFNEWRHAH 429 (497)
T ss_pred CCCCCCcCchHHHhhcCCCcccceeeccCccccCcHHHHHHhHHHHHhh
Confidence 9999999999999999999999999999999999999999999996433
No 2
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=100.00 E-value=3.7e-87 Score=657.78 Aligned_cols=378 Identities=19% Similarity=0.246 Sum_probs=327.5
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccchhhHHHHHHccCCCCCC
Q 013256 4 TLLEVTRAAHEEVERLERLVVKDLQTEPNSNKDRLVQSHRVRNMIDTITDTTERLIEIYADKDNARKDEIAALGGQTATG 83 (447)
Q Consensus 4 ~~LE~~R~~hEeiErlE~ai~~~l~~~p~t~k~~l~q~h~i~~~ld~~~~~~~~L~~~y~D~dg~r~~Ei~~l~g~~~~~ 83 (447)
++||+.|++|||+|+||+|||+|+++||+-.|+++...|.|+.|.......++.++--.+-.+|++.+++..|... .
T Consensus 2 nlLET~R~~~EEmE~ienAIaeR~~~NPK~Pr~~lrle~qi~~f~n~~R~~~q~~lv~hE~~~~lkDq~~~rinr~---~ 78 (470)
T COG5188 2 NLLETRRSLLEEMEIIENAIAERIQRNPKLPRDELRLERQIRIFENMERISNQIWLVEHERPTGLKDQMMKRINRS---I 78 (470)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhHHHHHHHHHHHhhhhhhhcccccchhHHHHHHHHHHH---h
Confidence 4999999999999999999999999999999999999999999999999999999999999999999999998620 1
Q ss_pred CchHHHHHHHHHHHHHhhhhCCCCccccCchhhHHhh-h---ccCCC--CcccccccCccccchHHHHHHHhcCCCCCcc
Q 013256 84 TNVFSSFYDRLKEIREYHRRHPSARVAVDASEDYENL-L---KEEPL--VEFSGEEAYGRYLDLHELYNQYINSKFGKEI 157 (447)
Q Consensus 84 ~~~f~~Fy~rL~~Ike~hr~~p~~~~~~~~~~~~~~~-~---~~~~~--~~Fs~EE~yGryLDL~~~y~~ylNl~~~~~i 157 (447)
++...+||..|++|..+|+.+|...| ......+... . ..++. ..|+|+|+||+|+||+++|..|+|+....+|
T Consensus 79 d~dl~~fykkLg~l~~e~K~~~e~~v-k~l~~l~~~~ss~p~~~dlD~~~~F~g~e~YG~~meLe~~~~~y~nv~~~~~~ 157 (470)
T COG5188 79 DRDLYGFYKKLGALNVEGKLDGEIEV-KGLRDLGYYESSAPKARDLDVEAAFKGSELYGDGMELERIFRKYANVHLCSDC 157 (470)
T ss_pred hhhhhHHHHHHHHHHHHhccCccccc-cchhhhhccccCCCCcccccHHHHhcchHhhcchhhHHHHHHHHhhHHhhccc
Confidence 46699999999999999999996544 2322221111 1 11122 3699999999999999999999999999999
Q ss_pred chhHHHhhhcCCCCCcccccchhhHHHHHHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHhhCCCCCCcccCcCCC
Q 013256 158 EYSAYLDVFSRPHEIPRKLKMTRQYREYIEKLLEYLIYFFQRTEPLQDLDRIFSKVVADFEEQWVTSTLQGWETEGQENG 237 (447)
Q Consensus 158 ~Yl~YL~~f~~f~~ip~~~K~~~~Y~~YL~~L~~YL~~F~~R~~PL~d~~~~~~~~~~~Fe~~W~~g~~~gW~~~~~~~~ 237 (447)
+|++||..+..|.-+|+..| |..|..||..|.+||.+||.+++||.+.+++.+.+.++|+..|+.| ++||.....
T Consensus 158 sylefLk~le~fd~~~~p~K-n~rY~~yl~~L~eYl~~F~~~~ypL~~~~kv~a~~~~~f~~a~~rG-~~~~~~~~g--- 232 (470)
T COG5188 158 SYLEFLKKLERFDLTTEPSK-NFRYLEYLSELNEYLGRFIKVKYPLKMFRKVVASAPKIFSRAEARG-FGKKNGMEG--- 232 (470)
T ss_pred hHHHHHHHHHHhhccCCccc-chhHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhchhHhHHHHHcc-CCcccccch---
Confidence 99999999999986754334 7899999999999999999999999999999999999999999999 889973211
Q ss_pred CCCCCCCccCccccchHHHHHhhchhhhhHHHHhcccCCCCchHHHHHHhhhhcCCCccchhhhhhhccCCCCCCCCCCC
Q 013256 238 HVPAQHSELDLDYYSTVEELMEVGSERLKEELAAKGLKSGGTLQQRAERLFLTKHTPLDKLDKKHFAKGARGKEQNGVAP 317 (447)
Q Consensus 238 ~~~~~~~~~~~~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~K~ra~rLf~~k~~~~e~~~~~~~ak~~~~~~~~~~~~ 317 (447)
......+||..|+++|+ +.+||..||+||.|.|+-..
T Consensus 233 -----~~~~~~~YC~~C~r~f~------~~~VFe~Hl~gK~H~k~~~~-------------------------------- 269 (470)
T COG5188 233 -----AEWFPKVYCVKCGREFS------RSKVFEYHLEGKRHCKEGQG-------------------------------- 269 (470)
T ss_pred -----hhhccceeeHhhhhHhh------hhHHHHHHHhhhhhhhhhhh--------------------------------
Confidence 01234599999999999 99999999999999985321
Q ss_pred cccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCHHHHHHHHHhhhh--------------hhcCCCCchh
Q 013256 318 ATQEVGNLKDIALMEAKMKKLCDLLSETIERTIQNVQKKQALTYEEMEAEREEQEE--------------TQVDTESDDE 383 (447)
Q Consensus 318 ~~~~~~~~k~ia~~E~~I~~l~e~L~~~~~~T~~nveRKqa~T~~Ere~E~e~~~~--------------~~~~~e~~de 383 (447)
...++..||.|++|+.+|.+++.+|+++|.|++|+|+.||.+|++.+.. .+..+.+.+|
T Consensus 270 -------~~~~v~~Ey~l~r~~kyl~d~~s~trs~V~r~la~ta~ER~aei~~l~r~~~~~at~S~e~EGaeq~d~eQ~D 342 (470)
T COG5188 270 -------KEEFVYSEYVLHRYLKYLGDPVSETRSLVLRSLAITAKERKAEISLLSRRKKQPATKSSEKEGAEQVDGEQRD 342 (470)
T ss_pred -------hhHHHHHHHHHHHHHHHhCChhHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhccCCCchhhcccccccccccc
Confidence 3459999999999999999999999999999999999999999987522 0112233556
Q ss_pred hhhhcCCCCCCCCCCCCCchhHHHHHhcCCceeeeeeccCcccchhhhHHHhhhhhh
Q 013256 384 EQQIYNPLKLPMGWDGKPIPYWLYKLHGLGQVFSSLNCYNLLQDLGFLWINVFYEEL 440 (447)
Q Consensus 384 e~~iyNPlnLPLGwDGkPIPyWLYKLhGL~~ey~CEICGN~~Y~Gr~~~~~~f~~~~ 440 (447)
++.+|||++|||||||+|||||||||||||++|.||||||++|+||++|+|||.|+-
T Consensus 343 E~~~~k~fdmPLG~DG~PmP~WL~klhgLd~ef~CEICgNyvy~GR~~FdrHF~E~r 399 (470)
T COG5188 343 EHVSGKSFDMPLGPDGLPMPRWLCKLHGLDIEFECEICGNYVYYGRDRFDRHFEEDR 399 (470)
T ss_pred hhhccCcccCCCCCCCCCCchHHHHhcCCCcceeeeecccccccchHHHHhhhhhhh
Confidence 788999999999999999999999999999999999999999999999999999974
No 3
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=100.00 E-value=3.6e-53 Score=396.23 Aligned_cols=112 Identities=52% Similarity=0.781 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCHHHHHHHHHhhhh--------------hhcCCCCchhhhhhcCCCCCC
Q 013256 329 ALMEAKMKKLCDLLSETIERTIQNVQKKQALTYEEMEAEREEQEE--------------TQVDTESDDEEQQIYNPLKLP 394 (447)
Q Consensus 329 a~~E~~I~~l~e~L~~~~~~T~~nveRKqa~T~~Ere~E~e~~~~--------------~~~~~e~~dee~~iyNPlnLP 394 (447)
|++|++|++|+++|++++++|++|||||||+|++||++|...... ...+++++|+++++|||+|||
T Consensus 1 ~~~E~~i~~~~~~L~~~~~~T~~~verk~a~T~~E~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~np~~lP 80 (196)
T PF11931_consen 1 ARREYKIHKLCELLSEEREDTKENVERKQARTEEERQAEEEYEEEIYSEDEYEEEEEEEESEEDSDDDEEEKIYNPLNLP 80 (196)
T ss_dssp -HHHHHHHHHHHHTHHHHHHHHHHHHHHHT--HHHHHHHHHHTS-SS-TT--SS--B-----------------------
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHhhhhhhhccccccccccccccccccccccccccCCcccCC
Confidence 678999999999999999999999999999999999997432100 112334466678899999999
Q ss_pred CCCCCCCchhHHHHHhcCCceeeeeeccCcccchhhhHHHhhhhhh
Q 013256 395 MGWDGKPIPYWLYKLHGLGQVFSSLNCYNLLQDLGFLWINVFYEEL 440 (447)
Q Consensus 395 LGwDGkPIPyWLYKLhGL~~ey~CEICGN~~Y~Gr~~~~~~f~~~~ 440 (447)
|||||||||||||||||||++|+||||||++|||||+|++||+||-
T Consensus 81 LG~DGkPIPyWLYKLhGL~~ey~CEICGN~~Y~GrkaFekHF~E~r 126 (196)
T PF11931_consen 81 LGWDGKPIPYWLYKLHGLGVEYKCEICGNQSYKGRKAFEKHFQEWR 126 (196)
T ss_dssp ----------------------------------------------
T ss_pred CCCCCCcccHHHHHHhCCCCeeeeEeCCCcceecHHHHHHhcChhH
Confidence 9999999999999999999999999999999999999999999985
No 4
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=99.59 E-value=9.7e-16 Score=117.30 Aligned_cols=59 Identities=59% Similarity=0.866 Sum_probs=56.4
Q ss_pred CccccchHHHHHhhchhhhhHHHHhcccCCCCchHHHHHHhhhhcCCCccchhhhhhhc
Q 013256 247 DLDYYSTVEELMEVGSERLKEELAAKGLKSGGTLQQRAERLFLTKHTPLDKLDKKHFAK 305 (447)
Q Consensus 247 ~~~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~K~ra~rLf~~k~~~~e~~~~~~~ak 305 (447)
|+..|++++.+.++|+||||+++++.|||||||+++||+|||++||++++++|+++|||
T Consensus 2 dL~~f~sa~eLe~lGldrLK~~L~a~GLKcGGTl~ERA~RLfs~kg~~~~~~d~~l~AK 60 (60)
T PF13297_consen 2 DLDAFSSAEELEALGLDRLKSALMALGLKCGGTLQERAARLFSVKGLPLEEIDKKLFAK 60 (60)
T ss_pred cchhcCCHHHHHHhCHHHHHHHHHHcCCccCCCHHHHHHHHHHhcCCChhhCCHHHhcC
Confidence 56788999999999999999999999999999999999999999999999999999885
No 5
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=98.92 E-value=6.9e-10 Score=72.99 Aligned_cols=23 Identities=65% Similarity=1.180 Sum_probs=18.6
Q ss_pred CchHHHHHHHHHHHHHhhhhCCC
Q 013256 84 TNVFSSFYDRLKEIREYHRRHPS 106 (447)
Q Consensus 84 ~~~f~~Fy~rL~~Ike~hr~~p~ 106 (447)
+|+|++||+||++|||||+||||
T Consensus 6 ~d~f~eFY~rlk~Ike~Hrr~Pn 28 (28)
T PF12108_consen 6 GDPFSEFYERLKEIKEYHRRYPN 28 (28)
T ss_dssp --HHHHHHHHHHHHHHHHHS--S
T ss_pred CChHHHHHHHHHHHHHHHHhCCC
Confidence 69999999999999999999996
No 6
>KOG2827 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.54 E-value=6.5e-08 Score=94.96 Aligned_cols=61 Identities=54% Similarity=0.837 Sum_probs=57.3
Q ss_pred ccCccccchHHHHHhhchhhhhHHHHhcccCCCCchHHHHHHhhhhcCCCccchhhhhhhc
Q 013256 245 ELDLDYYSTVEELMEVGSERLKEELAAKGLKSGGTLQQRAERLFLTKHTPLDKLDKKHFAK 305 (447)
Q Consensus 245 ~~~~~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~K~ra~rLf~~k~~~~e~~~~~~~ak 305 (447)
++++..|.+...+.-|||+|||.+|...||||||++.+||.|||++|++|+.++|++++++
T Consensus 261 p~~~ddf~s~~d~e~lg~e~lk~~l~~rglkcgg~l~eraarl~~~k~~~~~~~pk~~l~~ 321 (322)
T KOG2827|consen 261 PLNFDDFNSPADMEVLGMERLKTELQSRGLKCGGTLRERAARLFLLKSTPLDKLPKKLLAK 321 (322)
T ss_pred CccccccCCHHHHHHhhHHHHHHHHHhcCCcccccHHHHHhhhhhhcCCChhhhhHhhccC
Confidence 6667778899999999999999999999999999999999999999999999999998775
No 7
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.57 E-value=0.0056 Score=39.69 Aligned_cols=26 Identities=15% Similarity=0.190 Sum_probs=24.3
Q ss_pred cccchHHHHHhhchhhhhHHHHhcccCCCCch
Q 013256 249 DYYSTVEELMEVGSERLKEELAAKGLKSGGTL 280 (447)
Q Consensus 249 ~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~ 280 (447)
.||..|++.|. ++..+..|+++++|+
T Consensus 2 ~~C~~C~k~f~------~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 2 FYCDACDKYFS------SENQLKQHMKSKKHK 27 (27)
T ss_dssp CBBTTTTBBBS------SHHHHHCCTTSHHHH
T ss_pred CCcccCCCCcC------CHHHHHHHHccCCCC
Confidence 68999999999 999999999998874
No 8
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=90.27 E-value=0.14 Score=32.02 Aligned_cols=21 Identities=14% Similarity=-0.075 Sum_probs=19.3
Q ss_pred eeeeeccCcccchhhhHHHhhh
Q 013256 416 FSSLNCYNLLQDLGFLWINVFY 437 (447)
Q Consensus 416 y~CEICGN~~Y~Gr~~~~~~f~ 437 (447)
|.|.|| |.++.++..|..|++
T Consensus 1 ~~C~~C-~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDIC-NKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTT-TEEESSHHHHHHHHT
T ss_pred CCCCCC-CCCcCCHHHHHHHHC
Confidence 789999 889999999999985
No 9
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=88.03 E-value=0.039 Score=34.67 Aligned_cols=25 Identities=16% Similarity=0.158 Sum_probs=22.8
Q ss_pred cccchHHHHHhhchhhhhHHHHhcccCCCCc
Q 013256 249 DYYSTVEELMEVGSERLKEELAAKGLKSGGT 279 (447)
Q Consensus 249 ~~c~sceklf~~g~~~lk~~v~~~hLk~kkh 279 (447)
.+|..|++.|. ..+.+..|+.|++|
T Consensus 1 ~~C~~C~~~f~------s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFS------SENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEES------SHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcC------CHHHHHHHHCcCCC
Confidence 37999999999 99999999999876
No 10
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=87.65 E-value=0.11 Score=35.17 Aligned_cols=29 Identities=14% Similarity=0.021 Sum_probs=26.5
Q ss_pred cccchHHHHHhhchhhhhHHHHhcccCCCCchHHH
Q 013256 249 DYYSTVEELMEVGSERLKEELAAKGLKSGGTLQQR 283 (447)
Q Consensus 249 ~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~K~r 283 (447)
.+|+.|++.|. ....+..|++|++|.+..
T Consensus 4 ~~C~~C~~~~~------~~~~~~~H~~gk~H~~~~ 32 (35)
T smart00451 4 FYCKLCNVTFT------DEISVEAHLKGKKHKKNV 32 (35)
T ss_pred eEccccCCccC------CHHHHHHHHChHHHHHHH
Confidence 79999999999 899999999999998754
No 11
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=86.29 E-value=0.21 Score=35.11 Aligned_cols=13 Identities=23% Similarity=0.718 Sum_probs=8.0
Q ss_pred CceeeeeeccCcc
Q 013256 413 GQVFSSLNCYNLL 425 (447)
Q Consensus 413 ~~ey~CEICGN~~ 425 (447)
..-|+|++|||.+
T Consensus 4 ~~~YkC~~CGniV 16 (36)
T PF06397_consen 4 GEFYKCEHCGNIV 16 (36)
T ss_dssp TEEEE-TTT--EE
T ss_pred ccEEEccCCCCEE
Confidence 4579999999975
No 12
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=83.63 E-value=3.3 Score=38.82 Aligned_cols=33 Identities=3% Similarity=-0.047 Sum_probs=28.2
Q ss_pred ccCccccchHHHHHhhchhhhhHHHHhcccCCCCchHHH
Q 013256 245 ELDLDYYSTVEELMEVGSERLKEELAAKGLKSGGTLQQR 283 (447)
Q Consensus 245 ~~~~~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~K~r 283 (447)
...+.||..|+=.+. -+.-|--|++||+|..+-
T Consensus 72 q~~GyyCdVCdcvvK------DSinflDHiNgKkHqrnl 104 (193)
T KOG4727|consen 72 QKGGYYCDVCDCVVK------DSINFLDHINGKKHQRNL 104 (193)
T ss_pred ccCceeeeecceeeh------hhHHHHHHhccHHHHHHH
Confidence 445599999999999 888999999999997643
No 13
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=79.11 E-value=0.89 Score=39.12 Aligned_cols=16 Identities=6% Similarity=0.110 Sum_probs=14.2
Q ss_pred ceeeeeeccCcccchh
Q 013256 414 QVFSSLNCYNLLQDLG 429 (447)
Q Consensus 414 ~ey~CEICGN~~Y~Gr 429 (447)
..++|=||||-+|||-
T Consensus 1 ~kWkC~iCg~~I~~gq 16 (101)
T PF09943_consen 1 KKWKCYICGKPIYEGQ 16 (101)
T ss_pred CceEEEecCCeeeecc
Confidence 3689999999999995
No 14
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.02 E-value=1.1 Score=34.24 Aligned_cols=32 Identities=13% Similarity=0.136 Sum_probs=26.8
Q ss_pred HHHHHhcCCceeeeeeccCcccchhhhHHHhh
Q 013256 405 WLYKLHGLGQVFSSLNCYNLLQDLGFLWINVF 436 (447)
Q Consensus 405 WLYKLhGL~~ey~CEICGN~~Y~Gr~~~~~~f 436 (447)
|=-=--|-++.-+|+-||-.+-.+|..|+|-.
T Consensus 24 wkIiRvGaDIkikC~nC~h~vm~pR~~Ferkl 55 (60)
T COG4481 24 WKIIRVGADIKIKCENCGHSVMMPRYDFERKL 55 (60)
T ss_pred EEEEEecCcEEEEecCCCcEEEecHHHHHHHH
Confidence 33334588999999999999999999999854
No 15
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=78.11 E-value=1.1 Score=27.29 Aligned_cols=21 Identities=5% Similarity=-0.146 Sum_probs=16.8
Q ss_pred eeeeeccCcccchhhhHHHhhh
Q 013256 416 FSSLNCYNLLQDLGFLWINVFY 437 (447)
Q Consensus 416 y~CEICGN~~Y~Gr~~~~~~f~ 437 (447)
|+|++||. +|.-+..+.+|-.
T Consensus 1 y~C~~C~~-~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGK-SFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTE-EESSHHHHHHHHH
T ss_pred CCCCCCCC-ccCCHHHHHHHHh
Confidence 89999985 6778888888853
No 16
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=77.74 E-value=0.82 Score=31.25 Aligned_cols=13 Identities=38% Similarity=0.741 Sum_probs=11.2
Q ss_pred CceeeeeeccCcc
Q 013256 413 GQVFSSLNCYNLL 425 (447)
Q Consensus 413 ~~ey~CEICGN~~ 425 (447)
..-|+|++|||.+
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 4579999999986
No 17
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=77.33 E-value=1.2 Score=47.36 Aligned_cols=86 Identities=10% Similarity=0.002 Sum_probs=59.2
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHhhCCCCCCcccCcCCCCCCCCCCccCccccchHH
Q 013256 176 LKMTRQYREYIEKLLEYLIYFFQRTEPLQDLDRIFSKVVADFEEQWVTSTLQGWETEGQENGHVPAQHSELDLDYYSTVE 255 (447)
Q Consensus 176 ~K~~~~Y~~YL~~L~~YL~~F~~R~~PL~d~~~~~~~~~~~Fe~~W~~g~~~gW~~~~~~~~~~~~~~~~~~~~~c~sce 255 (447)
...+.+|...+=-...|-+.|...+.-|.+.+....-+...|+....++.+-|- ...+.+|.-|+
T Consensus 214 ~~f~~~~~aG~lpg~~~~et~~~~~~dl~~~~s~Eel~~~g~erlk~al~algl---------------k~gGt~~~ra~ 278 (497)
T KOG2636|consen 214 KEFERAWAAGTLPGWKYKETFSAKALDLSGASSVEELYCLGCERLKSALTALGL---------------KCGGTLHERAQ 278 (497)
T ss_pred hHHHHHHHhCCCCCccccccccccccccchhhHHHHHHhhchhHHHHHHHHHHH---------------hcCCeecHHHH
Confidence 344567777777777888888888866666666655556667666666543321 12237899999
Q ss_pred HHHhhchhhhhHHHHhcccCCCCchHH
Q 013256 256 ELMEVGSERLKEELAAKGLKSGGTLQQ 282 (447)
Q Consensus 256 klf~~g~~~lk~~v~~~hLk~kkh~K~ 282 (447)
++|+ ..++.-.||.++-|.+.
T Consensus 279 rlf~------Tk~~~l~~L~~~~~~kn 299 (497)
T KOG2636|consen 279 RLFS------TKSKSLSHLDTKLFAKN 299 (497)
T ss_pred hhhh------hcCcchhhhhhhhhccC
Confidence 9999 88888888887655553
No 18
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=76.89 E-value=1.6 Score=26.16 Aligned_cols=21 Identities=10% Similarity=-0.168 Sum_probs=16.2
Q ss_pred eeeeeccCcccchhhhHHHhhh
Q 013256 416 FSSLNCYNLLQDLGFLWINVFY 437 (447)
Q Consensus 416 y~CEICGN~~Y~Gr~~~~~~f~ 437 (447)
|.|++|| .+|..+..+.+|..
T Consensus 1 ~~C~~C~-~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICG-KSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS--EESSHHHHHHHHH
T ss_pred CCCcCCC-CcCCcHHHHHHHHH
Confidence 7999996 67889999999975
No 19
>smart00355 ZnF_C2H2 zinc finger.
Probab=76.41 E-value=1.5 Score=26.48 Aligned_cols=21 Identities=5% Similarity=-0.039 Sum_probs=18.5
Q ss_pred eeeeeccCcccchhhhHHHhhh
Q 013256 416 FSSLNCYNLLQDLGFLWINVFY 437 (447)
Q Consensus 416 y~CEICGN~~Y~Gr~~~~~~f~ 437 (447)
|.|..|| .++.++..+.+|..
T Consensus 1 ~~C~~C~-~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECG-KVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCc-chhCCHHHHHHHHH
Confidence 6899999 77789999999975
No 20
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=76.37 E-value=1.6 Score=38.68 Aligned_cols=27 Identities=7% Similarity=-0.007 Sum_probs=26.1
Q ss_pred cccchHHHHHhhchhhhhHHHHhcccCCCCchH
Q 013256 249 DYYSTVEELMEVGSERLKEELAAKGLKSGGTLQ 281 (447)
Q Consensus 249 ~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~K 281 (447)
.||..|.+.|. .++++..|+++|.|++
T Consensus 58 fyCi~CaRyFi------~~~~l~~H~ktK~HKr 84 (129)
T KOG3408|consen 58 FYCIECARYFI------DAKALKTHFKTKVHKR 84 (129)
T ss_pred eehhhhhhhhc------chHHHHHHHhccHHHH
Confidence 89999999999 9999999999999987
No 21
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=75.57 E-value=1.2 Score=28.67 Aligned_cols=21 Identities=10% Similarity=-0.105 Sum_probs=19.0
Q ss_pred eeeeeccCcccchhhhHHHhhh
Q 013256 416 FSSLNCYNLLQDLGFLWINVFY 437 (447)
Q Consensus 416 y~CEICGN~~Y~Gr~~~~~~f~ 437 (447)
|.|++|+ ..+....+|++|..
T Consensus 2 ~~C~~C~-k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACD-KYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTT-BBBSSHHHHHCCTT
T ss_pred CCcccCC-CCcCCHHHHHHHHc
Confidence 7899999 88999999999964
No 22
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=75.56 E-value=1 Score=30.80 Aligned_cols=12 Identities=25% Similarity=0.575 Sum_probs=10.5
Q ss_pred ceeeeeeccCcc
Q 013256 414 QVFSSLNCYNLL 425 (447)
Q Consensus 414 ~ey~CEICGN~~ 425 (447)
.-|+|++|||.+
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 469999999986
No 23
>PLN02748 tRNA dimethylallyltransferase
Probab=73.56 E-value=1.7 Score=47.00 Aligned_cols=26 Identities=15% Similarity=0.093 Sum_probs=23.3
Q ss_pred CCceeeeeeccCcccchhhhHHHhhh
Q 013256 412 LGQVFSSLNCYNLLQDLGFLWINVFY 437 (447)
Q Consensus 412 L~~ey~CEICGN~~Y~Gr~~~~~~f~ 437 (447)
+-..|.|||||+.+-.|...|+.|+.
T Consensus 415 ~~~~~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 415 LWTQYVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred ccccccccCCCCcccCCHHHHHHHhc
Confidence 35789999999989999999999986
No 24
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=73.40 E-value=3.9 Score=35.52 Aligned_cols=30 Identities=17% Similarity=0.127 Sum_probs=26.6
Q ss_pred cccchHHHHHhhchhhhhHHHHhcccCCCCchHHHHH
Q 013256 249 DYYSTVEELMEVGSERLKEELAAKGLKSGGTLQQRAE 285 (447)
Q Consensus 249 ~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~K~ra~ 285 (447)
.||..|.+.|- .+.+..-|++|+-|++ |++
T Consensus 56 hYCieCaryf~------t~~aL~~HkkgkvHkR-R~K 85 (126)
T COG5112 56 HYCIECARYFI------TEKALMEHKKGKVHKR-RAK 85 (126)
T ss_pred eeeehhHHHHH------HHHHHHHHhccchhHH-HHH
Confidence 79999999999 9999999999999876 444
No 25
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=58.83 E-value=3.7 Score=29.04 Aligned_cols=33 Identities=3% Similarity=-0.027 Sum_probs=18.6
Q ss_pred cccchHHHHHhhchhhhhHHHHhcccCCCCchHHHHH
Q 013256 249 DYYSTVEELMEVGSERLKEELAAKGLKSGGTLQQRAE 285 (447)
Q Consensus 249 ~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~K~ra~ 285 (447)
.||+-|+.++.- =+.++-..|..|.+|+.+.+.
T Consensus 4 yyCdyC~~~~~~----d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 4 YYCDYCKKYLTH----DSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp -B-TTT--B-S------SHHHHHHHT--THHHHHHHH
T ss_pred eecccccceecC----CChHHHHHhhccHHHHHHHHH
Confidence 799999999930 034566899999999986643
No 26
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=57.90 E-value=6.6 Score=24.20 Aligned_cols=20 Identities=5% Similarity=0.014 Sum_probs=15.0
Q ss_pred eeeeeccCcccchhhhHHHhhh
Q 013256 416 FSSLNCYNLLQDLGFLWINVFY 437 (447)
Q Consensus 416 y~CEICGN~~Y~Gr~~~~~~f~ 437 (447)
|+|..|. ++-. +..+.+|..
T Consensus 1 y~C~~C~-y~t~-~~~l~~H~~ 20 (24)
T PF13909_consen 1 YKCPHCS-YSTS-KSNLKRHLK 20 (24)
T ss_dssp EE-SSSS--EES-HHHHHHHHH
T ss_pred CCCCCCC-CcCC-HHHHHHHHH
Confidence 8999999 5557 889999865
No 27
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=56.44 E-value=4.4 Score=27.90 Aligned_cols=15 Identities=13% Similarity=0.151 Sum_probs=10.7
Q ss_pred eeeeeeccCcccchhh
Q 013256 415 VFSSLNCYNLLQDLGF 430 (447)
Q Consensus 415 ey~CEICGN~~Y~Gr~ 430 (447)
.|.|.+|| ++|.|..
T Consensus 2 ~~~C~~CG-~i~~g~~ 16 (34)
T cd00729 2 VWVCPVCG-YIHEGEE 16 (34)
T ss_pred eEECCCCC-CEeECCc
Confidence 57888888 5666754
No 28
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=50.66 E-value=4.5 Score=43.39 Aligned_cols=31 Identities=16% Similarity=0.091 Sum_probs=29.4
Q ss_pred cccchHHHHHhhchhhhhHHHHhcccCCCCchHHHHH
Q 013256 249 DYYSTVEELMEVGSERLKEELAAKGLKSGGTLQQRAE 285 (447)
Q Consensus 249 ~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~K~ra~ 285 (447)
.||.+|+|-|. ++.-+.+|-++|+|++..+.
T Consensus 293 lyC~vCnKsFK------seKq~kNHEnSKKHkenv~e 323 (508)
T KOG0717|consen 293 LYCVVCNKSFK------SEKQLKNHENSKKHKENVAE 323 (508)
T ss_pred eEEeecccccc------chHHHHhhHHHHHHHHHHHH
Confidence 89999999999 99999999999999998775
No 29
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=48.31 E-value=11 Score=24.10 Aligned_cols=17 Identities=12% Similarity=0.171 Sum_probs=13.2
Q ss_pred HHhcCCceeeeeeccCc
Q 013256 408 KLHGLGQVFSSLNCYNL 424 (447)
Q Consensus 408 KLhGL~~ey~CEICGN~ 424 (447)
+.|-=.+.|+|.+||..
T Consensus 7 ~~H~~~k~~~C~~C~k~ 23 (26)
T PF13465_consen 7 RTHTGEKPYKCPYCGKS 23 (26)
T ss_dssp HHHSSSSSEEESSSSEE
T ss_pred hhcCCCCCCCCCCCcCe
Confidence 35666789999999853
No 30
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=42.67 E-value=13 Score=23.71 Aligned_cols=20 Identities=5% Similarity=-0.308 Sum_probs=16.3
Q ss_pred eeeeeccCcccchhhhHHHhhh
Q 013256 416 FSSLNCYNLLQDLGFLWINVFY 437 (447)
Q Consensus 416 y~CEICGN~~Y~Gr~~~~~~f~ 437 (447)
.+|.+||..- ++.++++|..
T Consensus 3 ~~C~~CgR~F--~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF--NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE--CHHHHHHHHH
Confidence 4799999754 9999999953
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=41.45 E-value=14 Score=23.24 Aligned_cols=21 Identities=10% Similarity=-0.167 Sum_probs=16.8
Q ss_pred eeeeeeccCcccchhhhHHHhh
Q 013256 415 VFSSLNCYNLLQDLGFLWINVF 436 (447)
Q Consensus 415 ey~CEICGN~~Y~Gr~~~~~~f 436 (447)
.|+|.+||. +|....+|..|=
T Consensus 1 ~~~C~~C~~-~F~~~~~l~~H~ 21 (27)
T PF13912_consen 1 PFECDECGK-TFSSLSALREHK 21 (27)
T ss_dssp SEEETTTTE-EESSHHHHHHHH
T ss_pred CCCCCccCC-ccCChhHHHHHh
Confidence 489999975 677888888874
No 32
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=40.46 E-value=11 Score=25.59 Aligned_cols=14 Identities=14% Similarity=0.095 Sum_probs=10.1
Q ss_pred eeeeeccCcccchhh
Q 013256 416 FSSLNCYNLLQDLGF 430 (447)
Q Consensus 416 y~CEICGN~~Y~Gr~ 430 (447)
|.|-+|| ++|.|.+
T Consensus 2 ~~C~~CG-y~y~~~~ 15 (33)
T cd00350 2 YVCPVCG-YIYDGEE 15 (33)
T ss_pred EECCCCC-CEECCCc
Confidence 7899998 5566654
No 33
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=38.94 E-value=21 Score=27.48 Aligned_cols=28 Identities=14% Similarity=0.080 Sum_probs=24.1
Q ss_pred cCCceeeeeeccCcccchhhhHHHhhhh
Q 013256 411 GLGQVFSSLNCYNLLQDLGFLWINVFYE 438 (447)
Q Consensus 411 GL~~ey~CEICGN~~Y~Gr~~~~~~f~~ 438 (447)
=..+.|.|..||=.+|--+.+|..=++|
T Consensus 10 ~~~v~~~Cp~cGipthcS~ehw~~D~e~ 37 (55)
T PF13824_consen 10 PAHVNFECPDCGIPTHCSEEHWEDDYEE 37 (55)
T ss_pred ccccCCcCCCCCCcCccCHHHHHHhHHH
Confidence 4579999999999999999998776655
No 34
>PRK12496 hypothetical protein; Provisional
Probab=38.46 E-value=7 Score=36.36 Aligned_cols=26 Identities=12% Similarity=0.162 Sum_probs=22.0
Q ss_pred hHHHHHhcCCceee-------eeeccCcccchh
Q 013256 404 YWLYKLHGLGQVFS-------SLNCYNLLQDLG 429 (447)
Q Consensus 404 yWLYKLhGL~~ey~-------CEICGN~~Y~Gr 429 (447)
.|-|.=.|=+.+|+ |+|||+..-+-+
T Consensus 125 ~w~~~C~gC~~~~~~~~~~~~C~~CG~~~~r~~ 157 (164)
T PRK12496 125 KWRKVCKGCKKKYPEDYPDDVCEICGSPVKRKM 157 (164)
T ss_pred eeeEECCCCCccccCCCCCCcCCCCCChhhhcc
Confidence 59999999999994 999999875544
No 35
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=35.65 E-value=79 Score=24.03 Aligned_cols=13 Identities=46% Similarity=0.703 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHH
Q 013256 6 LEVTRAAHEEVER 18 (447)
Q Consensus 6 LE~~R~~hEeiEr 18 (447)
+|.||.+||.+|+
T Consensus 12 mEvQrrLhEQLEv 24 (51)
T PF14379_consen 12 MEVQRRLHEQLEV 24 (51)
T ss_pred HHHHHHHHHHHHH
Confidence 7999999999994
No 36
>PF03941 INCENP_ARK-bind: Inner centromere protein, ARK binding region; InterPro: IPR005635 This region of the inner centromere protein has been found to be necessary and sufficient for binding to aurora-related kinase. This interaction has been implicated in the coordination of chromosome segregation with cell division in yeast [].; PDB: 2BFX_C 2BFY_C 3ZTX_D 2VGO_D 2VGP_D 2VRX_D 4AF3_D.
Probab=32.78 E-value=15 Score=28.06 Aligned_cols=8 Identities=63% Similarity=1.373 Sum_probs=1.9
Q ss_pred CCCCchhH
Q 013256 398 DGKPIPYW 405 (447)
Q Consensus 398 DGkPIPyW 405 (447)
.+|+||-|
T Consensus 14 ~~k~iP~W 21 (57)
T PF03941_consen 14 PRKPIPSW 21 (57)
T ss_dssp ------GG
T ss_pred ccCCCCCC
Confidence 37999999
No 37
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=30.30 E-value=24 Score=22.64 Aligned_cols=13 Identities=23% Similarity=0.212 Sum_probs=11.0
Q ss_pred cCCceeeeeeccC
Q 013256 411 GLGQVFSSLNCYN 423 (447)
Q Consensus 411 GL~~ey~CEICGN 423 (447)
+.++.|+|.-||.
T Consensus 12 ~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 12 EQAVPFPCPNCGF 24 (24)
T ss_pred ccCceEeCCCCCC
Confidence 4589999999994
No 38
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=29.95 E-value=1.2e+02 Score=29.89 Aligned_cols=23 Identities=17% Similarity=0.348 Sum_probs=20.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Q 013256 5 LLEVTRAAHEEVERLERLVVKDL 27 (447)
Q Consensus 5 ~LE~~R~~hEeiErlE~ai~~~l 27 (447)
.+|..|.+|+||..||..|.+.-
T Consensus 51 h~eeLrqI~~DIn~lE~iIkqa~ 73 (230)
T PF10146_consen 51 HVEELRQINQDINTLENIIKQAE 73 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999988743
No 39
>COG4105 ComL DNA uptake lipoprotein [General function prediction only]
Probab=29.74 E-value=79 Score=31.69 Aligned_cols=40 Identities=18% Similarity=0.173 Sum_probs=22.0
Q ss_pred ccchHHHHHHHhcCCC-CCccchhHHHhhhcCCCCCccccc
Q 013256 138 YLDLHELYNQYINSKF-GKEIEYSAYLDVFSRPHEIPRKLK 177 (447)
Q Consensus 138 yLDL~~~y~~ylNl~~-~~~i~Yl~YL~~f~~f~~ip~~~K 177 (447)
|-+=-..-++||.+.. ...++|+.||..+..|..||...+
T Consensus 87 y~~A~~~~drFi~lyP~~~n~dY~~YlkgLs~~~~i~~~~r 127 (254)
T COG4105 87 YDLALAYIDRFIRLYPTHPNADYAYYLKGLSYFFQIDDVTR 127 (254)
T ss_pred HHHHHHHHHHHHHhCCCCCChhHHHHHHHHHHhccCCcccc
Confidence 3333334455655533 245777777776666666655444
No 40
>PF13319 DUF4090: Protein of unknown function (DUF4090)
Probab=29.18 E-value=25 Score=28.94 Aligned_cols=12 Identities=42% Similarity=0.794 Sum_probs=9.5
Q ss_pred CCCCCCCchhHH
Q 013256 395 MGWDGKPIPYWL 406 (447)
Q Consensus 395 LGwDGkPIPyWL 406 (447)
+..||.|||-=.
T Consensus 13 iDlDGspIP~~~ 24 (84)
T PF13319_consen 13 IDLDGSPIPPAM 24 (84)
T ss_pred cCCCCCcCCHHH
Confidence 578999999643
No 41
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=28.35 E-value=4.3e+02 Score=29.33 Aligned_cols=89 Identities=18% Similarity=0.267 Sum_probs=60.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH---HhhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccchhhHHHHHHccCCCC
Q 013256 5 LLEVTRAAHEEVERLERLVVKD---LQTEPNSNKDRLVQSHRVRNMIDTITDTTERLIEIYADKDNARKDEIAALGGQTA 81 (447)
Q Consensus 5 ~LE~~R~~hEeiErlE~ai~~~---l~~~p~t~k~~l~q~h~i~~~ld~~~~~~~~L~~~y~D~dg~r~~Ei~~l~g~~~ 81 (447)
-++.+|.+.+.++.|+...... +.......- ....++..+.+++....+...++.+.=+++|++|..+-
T Consensus 342 e~~~~~~l~~~l~~l~~~~~~~~~~i~~~~~~yS---~i~~~l~~~~~~l~~ie~~q~~~~~~l~~L~~dE~~Ar----- 413 (560)
T PF06160_consen 342 ELEIVRELEKQLKELEKRYEDLEERIEEQQVPYS---EIQEELEEIEEQLEEIEEEQEEINESLQSLRKDEKEAR----- 413 (560)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcCHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----
Confidence 4678888888888877765543 322222221 22345566666777777777777777788888998873
Q ss_pred CCCchHHHHHHHHHHHHHhhhhC
Q 013256 82 TGTNVFSSFYDRLKEIREYHRRH 104 (447)
Q Consensus 82 ~~~~~f~~Fy~rL~~Ike~hr~~ 104 (447)
.....|-..|..|+-+-.+.
T Consensus 414 ---~~l~~~~~~l~~ikR~lek~ 433 (560)
T PF06160_consen 414 ---EKLQKLKQKLREIKRRLEKS 433 (560)
T ss_pred ---HHHHHHHHHHHHHHHHHHHc
Confidence 44889999999999877664
No 42
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=27.67 E-value=23 Score=26.35 Aligned_cols=15 Identities=13% Similarity=0.115 Sum_probs=11.7
Q ss_pred eeeeeeccCcccchhh
Q 013256 415 VFSSLNCYNLLQDLGF 430 (447)
Q Consensus 415 ey~CEICGN~~Y~Gr~ 430 (447)
.|.|.+|| ++|-..+
T Consensus 1 ky~C~~Cg-yvYd~~~ 15 (47)
T PF00301_consen 1 KYQCPVCG-YVYDPEK 15 (47)
T ss_dssp EEEETTTS-BEEETTT
T ss_pred CcCCCCCC-EEEcCCc
Confidence 38999999 8886544
No 43
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=26.81 E-value=22 Score=26.74 Aligned_cols=14 Identities=14% Similarity=0.244 Sum_probs=11.4
Q ss_pred eeeeeeccCcccchh
Q 013256 415 VFSSLNCYNLLQDLG 429 (447)
Q Consensus 415 ey~CEICGN~~Y~Gr 429 (447)
.|.|-+|| ++|...
T Consensus 1 ~y~C~~Cg-yiYd~~ 14 (50)
T cd00730 1 KYECRICG-YIYDPA 14 (50)
T ss_pred CcCCCCCC-eEECCC
Confidence 38999999 899753
No 44
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=26.73 E-value=21 Score=25.42 Aligned_cols=10 Identities=30% Similarity=0.079 Sum_probs=4.4
Q ss_pred eeeeeccCcc
Q 013256 416 FSSLNCYNLL 425 (447)
Q Consensus 416 y~CEICGN~~ 425 (447)
-.|++|||.+
T Consensus 18 ~~C~~C~nls 27 (41)
T PF02132_consen 18 KFCSICGNLS 27 (41)
T ss_dssp EE-SSS--EE
T ss_pred CccCCCCCcC
Confidence 3577777765
No 45
>KOG0324 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.11 E-value=22 Score=34.55 Aligned_cols=20 Identities=35% Similarity=0.624 Sum_probs=17.0
Q ss_pred CCCchhHHHHHhcCCceeee
Q 013256 399 GKPIPYWLYKLHGLGQVFSS 418 (447)
Q Consensus 399 GkPIPyWLYKLhGL~~ey~C 418 (447)
|||||-|.-.|.-++..+.|
T Consensus 126 gk~IP~winrLa~~~~~~~~ 145 (214)
T KOG0324|consen 126 GKKIPSWVNRLARAGLCSLC 145 (214)
T ss_pred CCCccHHHHHHHHHhhhhHH
Confidence 99999999999988866444
No 46
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.96 E-value=28 Score=29.74 Aligned_cols=16 Identities=6% Similarity=0.127 Sum_probs=13.1
Q ss_pred ceeeeeeccCcccchh
Q 013256 414 QVFSSLNCYNLLQDLG 429 (447)
Q Consensus 414 ~ey~CEICGN~~Y~Gr 429 (447)
.+|+|=|||+.+--|-
T Consensus 5 kewkC~VCg~~iieGq 20 (103)
T COG4847 5 KEWKCYVCGGTIIEGQ 20 (103)
T ss_pred ceeeEeeeCCEeeecc
Confidence 5899999999876554
No 47
>PF09388 SpoOE-like: Spo0E like sporulation regulatory protein; InterPro: IPR018540 Spore formation is an extreme response to starvation and can also be a component of disease transmission. Sporulation is controlled by an expanded two-component system where starvation signals result in sensor kinase activation and phosphorylation of the master sporulation response regulator Spo0A. Phosphatases such as Spo0E dephosphorylate Spo0A thereby inhibiting sporulation. This is a family of Spo0E-like phosphatases. The structure of a Bacillus anthracis member of this family has revealed an anti-parallel alpha-helical structure []. ; PDB: 2BZB_B 2C0S_A.
Probab=25.38 E-value=2.6e+02 Score=20.07 Aligned_cols=42 Identities=17% Similarity=0.219 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHhhCCCChhHHHHHHHHHHHHHHHHHH
Q 013256 12 AHEEVERLERLVVKDLQTEPNSNKDRLVQSHRVRNMIDTITD 53 (447)
Q Consensus 12 ~hEeiErlE~ai~~~l~~~p~t~k~~l~q~h~i~~~ld~~~~ 53 (447)
+..+||.+-+.+........-+..+.|....++..++..|+.
T Consensus 2 L~~~Ie~~R~~L~~~~~~~~l~~~~vl~~Sq~LD~lI~~y~~ 43 (45)
T PF09388_consen 2 LLEEIEELRQELNELAEKKGLTDPEVLELSQELDKLINEYQK 43 (45)
T ss_dssp HHHHHHHHHHHHHHHHHHCCTTCHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhh
Confidence 567888888888887777676888899888899888888874
No 48
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=24.21 E-value=31 Score=32.23 Aligned_cols=32 Identities=3% Similarity=-0.012 Sum_probs=24.7
Q ss_pred cccchHHHHHhhchhhhhHHHHhcccCCCCchHHHH
Q 013256 249 DYYSTVEELMEVGSERLKEELAAKGLKSGGTLQQRA 284 (447)
Q Consensus 249 ~~c~sceklf~~g~~~lk~~v~~~hLk~kkh~K~ra 284 (447)
.||+.|+.+-.- | +.+|-..|+.|.+|+++.+
T Consensus 4 YyCDYCdt~Lth--D--slsvRK~H~~GrkH~~nvk 35 (165)
T KOG3454|consen 4 YYCDYCDTYLTH--D--SLSVRKTHCGGRKHKDNVK 35 (165)
T ss_pred chhhhhhhhhhc--c--cHHHHHhhhhhHHHHHHHH
Confidence 799999954420 1 6789999999999999654
No 49
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=23.94 E-value=5.4e+02 Score=28.48 Aligned_cols=90 Identities=17% Similarity=0.283 Sum_probs=52.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHh---hCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccchhhHHHHHHccCCC
Q 013256 4 TLLEVTRAAHEEVERLERLVVKDLQ---TEPNSNKDRLVQSHRVRNMIDTITDTTERLIEIYADKDNARKDEIAALGGQT 80 (447)
Q Consensus 4 ~~LE~~R~~hEeiErlE~ai~~~l~---~~p~t~k~~l~q~h~i~~~ld~~~~~~~~L~~~y~D~dg~r~~Ei~~l~g~~ 80 (447)
.-++..|.+.++|+.++..+..... ....... ..+.+...+.++....-+.-.++.+.-.+.|+.|..+-
T Consensus 345 ~e~~~~~~lekeL~~Le~~~~~~~~~i~~~~~~ys---el~e~leel~e~leeie~eq~ei~e~l~~Lrk~E~eAr---- 417 (569)
T PRK04778 345 SELESVRQLEKQLESLEKQYDEITERIAEQEIAYS---ELQEELEEILKQLEEIEKEQEKLSEMLQGLRKDELEAR---- 417 (569)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----
Confidence 4478889999999998888775432 2222211 11223333333444444444444444456777777664
Q ss_pred CCCCchHHHHHHHHHHHHHhhhhC
Q 013256 81 ATGTNVFSSFYDRLKEIREYHRRH 104 (447)
Q Consensus 81 ~~~~~~f~~Fy~rL~~Ike~hr~~ 104 (447)
+....|-..|..|+.+-++.
T Consensus 418 ----~kL~~~~~~L~~ikr~l~k~ 437 (569)
T PRK04778 418 ----EKLERYRNKLHEIKRYLEKS 437 (569)
T ss_pred ----HHHHHHHHHHHHHHHHHHHc
Confidence 33778888898888876664
No 50
>COG3502 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.89 E-value=44 Score=29.27 Aligned_cols=17 Identities=47% Similarity=0.766 Sum_probs=14.4
Q ss_pred hcCCCC---------CCCCCCCCCch
Q 013256 387 IYNPLK---------LPMGWDGKPIP 403 (447)
Q Consensus 387 iyNPln---------LPLGwDGkPIP 403 (447)
+|.||+ ||+|.||.+.+
T Consensus 86 LYgpL~l~AV~~~~pl~l~~DG~~~~ 111 (115)
T COG3502 86 LYGPLPLDAVTWVAPLPLGADGLFQF 111 (115)
T ss_pred cccccchhHheecccCCCCCCCCCCC
Confidence 688887 89999998764
No 51
>PRK13694 hypothetical protein; Provisional
Probab=23.28 E-value=1.9e+02 Score=24.23 Aligned_cols=18 Identities=44% Similarity=0.375 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 013256 6 LEVTRAAHEEVERLERLV 23 (447)
Q Consensus 6 LE~~R~~hEeiErlE~ai 23 (447)
-++.|++-|=|||||...
T Consensus 11 ~~~Lr~fIERIERLEeEk 28 (83)
T PRK13694 11 KEQLRAFIERIERLEEEK 28 (83)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 588999999999998653
No 52
>PRK06835 DNA replication protein DnaC; Validated
Probab=23.00 E-value=2.3e+02 Score=29.21 Aligned_cols=17 Identities=12% Similarity=0.045 Sum_probs=14.7
Q ss_pred CCceeeeeeccCcccch
Q 013256 412 LGQVFSSLNCYNLLQDL 428 (447)
Q Consensus 412 L~~ey~CEICGN~~Y~G 428 (447)
|...|.|.+|++..|=|
T Consensus 95 l~~~y~Cp~C~dtG~i~ 111 (329)
T PRK06835 95 LEMKYTCPKCKDTGFIN 111 (329)
T ss_pred cCCCCCCCCCCCCCCcC
Confidence 47789999999999965
No 53
>KOG2476 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.16 E-value=22 Score=38.41 Aligned_cols=42 Identities=17% Similarity=-0.114 Sum_probs=29.5
Q ss_pred CCCCCCCCCCchhHH-HHHhcCC-----ceeeeeeccCcccchhhhHH
Q 013256 392 KLPMGWDGKPIPYWL-YKLHGLG-----QVFSSLNCYNLLQDLGFLWI 433 (447)
Q Consensus 392 nLPLGwDGkPIPyWL-YKLhGL~-----~ey~CEICGN~~Y~Gr~~~~ 433 (447)
++-.|-++-|||-.+ ---.++. -.+-||||-|-+|.|++.+=
T Consensus 56 ~ykng~~~vPiptY~~g~~~~~~~ky~~n~~g~Ei~~Nlt~Lg~~G~~ 103 (528)
T KOG2476|consen 56 KYKNGTKKVPIPTYFLGDNANETEKYFENSDGKEIAENLTYLGRKGTY 103 (528)
T ss_pred HHhcCCccCceeEEEecCCCCccceecccCCCcccccceeeecccceE
Confidence 455788899999433 3223221 34789999999999998753
No 54
>TIGR00009 L28 ribosomal protein L28. This model describes bacterial and chloroplast forms of the 50S ribosomal protein L28, a polypeptide about 60 amino acids in length. Mitochondrial homologs differ substantially in architecture and are not included.
Probab=21.99 E-value=37 Score=26.03 Aligned_cols=16 Identities=0% Similarity=-0.504 Sum_probs=13.2
Q ss_pred eeeeeccCcccchhhh
Q 013256 416 FSSLNCYNLLQDLGFL 431 (447)
Q Consensus 416 y~CEICGN~~Y~Gr~~ 431 (447)
-.|||||-.+..|..+
T Consensus 3 ~~C~i~GK~~~~Gn~v 18 (56)
T TIGR00009 3 RKCQLTGKGPLSGNNV 18 (56)
T ss_pred CEeeeCCCcCccCCee
Confidence 4699999998888764
No 55
>PF09620 Cas_csx3: CRISPR-associated protein (Cas_csx3); InterPro: IPR013409 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 tha Csx3 family of Cas proteins, which is encoded in CRISPR-associated gene cluster near CRISPR repeats in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3).
Probab=21.96 E-value=61 Score=26.86 Aligned_cols=19 Identities=42% Similarity=0.945 Sum_probs=15.1
Q ss_pred CCCCCCCCCCCC-------CchhHHH
Q 013256 389 NPLKLPMGWDGK-------PIPYWLY 407 (447)
Q Consensus 389 NPlnLPLGwDGk-------PIPyWLY 407 (447)
+-++||.|-|.+ +.|.|||
T Consensus 15 ~~i~lP~~v~~~~GVVlsGr~PiWLy 40 (80)
T PF09620_consen 15 KGIELPAGVDPQKGVVLSGRAPIWLY 40 (80)
T ss_pred cccCCCCcCCCCceEEEECCccHHHH
Confidence 446799988865 6899998
No 56
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=21.45 E-value=57 Score=26.19 Aligned_cols=24 Identities=8% Similarity=-0.022 Sum_probs=21.1
Q ss_pred eeeeeeccCcccchhhhHHHhhhhh
Q 013256 415 VFSSLNCYNLLQDLGFLWINVFYEE 439 (447)
Q Consensus 415 ey~CEICGN~~Y~Gr~~~~~~f~~~ 439 (447)
.+.|-+||-. +..+.++..|....
T Consensus 50 ~~~C~~C~~~-f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKT-FRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-E-ESSHHHHHHHHHHT
T ss_pred CCCCCccCCC-CcCHHHHHHHHcCc
Confidence 8999999988 99999999999864
No 57
>PHA02768 hypothetical protein; Provisional
Probab=20.99 E-value=33 Score=26.39 Aligned_cols=20 Identities=10% Similarity=-0.009 Sum_probs=12.6
Q ss_pred eeeeeeccCcccchhhhHHHh
Q 013256 415 VFSSLNCYNLLQDLGFLWINV 435 (447)
Q Consensus 415 ey~CEICGN~~Y~Gr~~~~~~ 435 (447)
-|.|++||..-- =+.++.+|
T Consensus 5 ~y~C~~CGK~Fs-~~~~L~~H 24 (55)
T PHA02768 5 GYECPICGEIYI-KRKSMITH 24 (55)
T ss_pred ccCcchhCCeec-cHHHHHHH
Confidence 489999997644 33344444
No 58
>PF10102 DUF2341: Domain of unknown function (DUF2341); InterPro: IPR018765 This domain of unknown function is found in various bacterial proteins, including MotA/TolQ/ExbB proton channels and other transport proteins.
Probab=20.86 E-value=21 Score=29.93 Aligned_cols=14 Identities=43% Similarity=1.134 Sum_probs=11.5
Q ss_pred CCCCCCchhHHHHH
Q 013256 396 GWDGKPIPYWLYKL 409 (447)
Q Consensus 396 GwDGkPIPyWLYKL 409 (447)
+-||.|||||+-+.
T Consensus 10 d~~~~~L~ywIE~w 23 (89)
T PF10102_consen 10 DSDGTPLPYWIESW 23 (89)
T ss_pred eCCCCEeEEEEEEC
Confidence 56899999998764
No 59
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=20.44 E-value=17 Score=33.65 Aligned_cols=31 Identities=19% Similarity=0.279 Sum_probs=19.3
Q ss_pred CCCCCCchhHHHHHhcCC--ceeeeeeccCcccchhhhHH
Q 013256 396 GWDGKPIPYWLYKLHGLG--QVFSSLNCYNLLQDLGFLWI 433 (447)
Q Consensus 396 GwDGkPIPyWLYKLhGL~--~ey~CEICGN~~Y~Gr~~~~ 433 (447)
.+.|+|+ |.....-.. ..-+|+.|| |+++||
T Consensus 78 ~~gG~PL--w~s~~~~~~~~~ip~C~~Cg-----~~R~FE 110 (164)
T PF04194_consen 78 CRGGKPL--WISSTPIPPESDIPKCENCG-----SPRVFE 110 (164)
T ss_pred CCCCeEE--EecCCCCCccccCCCCccCC-----CccEEE
Confidence 5678855 655433222 256899999 666665
No 60
>PF01348 Intron_maturas2: Type II intron maturase; InterPro: IPR002866 Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA []. Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. These introns are found in plant organelles []. Maturases in higher plants are encoded for in the nuclear genes [] but are otherwise encoded by organellar introns. The Maturase-related, N-terminal domain is found in plant potential maturases, which probably assists in the splicing of chloroplast group II introns []. The function of this region is, however, unknown It has been shown that a specific region of the aI2 intron is needed for the maturase function []. This C-terminal region was found to be conserved in group II introns and called domain X [].; GO: 0006397 mRNA processing, 0009507 chloroplast
Probab=20.39 E-value=37 Score=30.77 Aligned_cols=25 Identities=20% Similarity=0.268 Sum_probs=16.1
Q ss_pred CCCCCchhHHHHHhcCCceeeeeeccC
Q 013256 397 WDGKPIPYWLYKLHGLGQVFSSLNCYN 423 (447)
Q Consensus 397 wDGkPIPyWLYKLhGL~~ey~CEICGN 423 (447)
.|+-|.++|-- ...-..=+|||||-
T Consensus 121 ~~~~~~~~~~~--~~~~~~~~C~lCg~ 145 (146)
T PF01348_consen 121 IDQFPRTYWYL--RTRLKARKCELCGS 145 (146)
T ss_pred ccccccccccc--ccccCCCEEEEeee
Confidence 34555555544 44667779999993
No 61
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=20.34 E-value=3.9e+02 Score=28.52 Aligned_cols=86 Identities=24% Similarity=0.272 Sum_probs=38.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH---HhhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccchhhHHHHHHccCCCC
Q 013256 5 LLEVTRAAHEEVERLERLVVKD---LQTEPNSNKDRLVQSHRVRNMIDTITDTTERLIEIYADKDNARKDEIAALGGQTA 81 (447)
Q Consensus 5 ~LE~~R~~hEeiErlE~ai~~~---l~~~p~t~k~~l~q~h~i~~~ld~~~~~~~~L~~~y~D~dg~r~~Ei~~l~g~~~ 81 (447)
++|..+.+-+...+|+..|-+. ++++- .-....-++-+.=.++..+....+.++..++=-.-|+|++.+..
T Consensus 217 ~~~el~eik~~~~~L~~~~e~Lk~~~~~e~---~~~~~~LqEEr~R~erLEeqlNd~~elHq~Ei~~LKqeLa~~EE--- 290 (395)
T PF10267_consen 217 ILEELREIKESQSRLEESIEKLKEQYQREY---QFILEALQEERYRYERLEEQLNDLTELHQNEIYNLKQELASMEE--- 290 (395)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH---
Confidence 4566666666666665555442 11111 11111222333334455555555666655544444444444322
Q ss_pred CCCchHHHHHHHHHHHHH
Q 013256 82 TGTNVFSSFYDRLKEIRE 99 (447)
Q Consensus 82 ~~~~~f~~Fy~rL~~Ike 99 (447)
-+=--.|+|.++|.|
T Consensus 291 ---K~~Yqs~eRaRdi~E 305 (395)
T PF10267_consen 291 ---KMAYQSYERARDIWE 305 (395)
T ss_pred ---HHHHHHHHHHhHHHH
Confidence 112245566666655
No 62
>PF10073 DUF2312: Uncharacterized protein conserved in bacteria (DUF2312); InterPro: IPR018753 This entry is represented by Azospirillum phage Cd, Gp10. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family of hypothetical bacterial proteins have no known function.
Probab=20.29 E-value=2.4e+02 Score=23.12 Aligned_cols=19 Identities=37% Similarity=0.310 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 013256 7 EVTRAAHEEVERLERLVVK 25 (447)
Q Consensus 7 E~~R~~hEeiErlE~ai~~ 25 (447)
++.|+.-|-|||||..+..
T Consensus 4 ~~Lr~~ieRiErLEeEk~~ 22 (74)
T PF10073_consen 4 EQLRQFIERIERLEEEKKA 22 (74)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5677888888888765443
No 63
>PF06290 PsiB: Plasmid SOS inhibition protein (PsiB); InterPro: IPR009385 This family consists of several plasmid SOS inhibition protein (PsiB) sequences [].; PDB: 3NCT_B.
Probab=20.12 E-value=47 Score=30.30 Aligned_cols=59 Identities=19% Similarity=0.248 Sum_probs=27.6
Q ss_pred HHHHHHHhhhcCHHHHHHHHHhhhhhhcCCCCchhhhhhcCCCCCCCCCCCCCchhHHHHHhcCCceeeeeeccCcc
Q 013256 349 TIQNVQKKQALTYEEMEAEREEQEETQVDTESDDEEQQIYNPLKLPMGWDGKPIPYWLYKLHGLGQVFSSLNCYNLL 425 (447)
Q Consensus 349 T~~nveRKqa~T~~Ere~E~e~~~~~~~~~e~~dee~~iyNPlnLPLGwDGkPIPyWLYKLhGL~~ey~CEICGN~~ 425 (447)
|+-+.+.-+++|+.|.|+=.+. -++.- =.-...+-+-|.+|=||+ .+-||.||.||=+.
T Consensus 3 ~~ltl~~L~tm~a~elE~~R~~-Ged~R----R~L~~aVm~~L~~P~gW~-------------~n~Ey~~EFgGffP 61 (143)
T PF06290_consen 3 TELTLEVLKTMSAQELEDYRAA-GEDFR----RELTHAVMRELTLPEGWR-------------VNAEYRSEFGGFFP 61 (143)
T ss_dssp ----HHHHHH--HHHHHHHHHH--HHHH----HHHHHHHHHT----TTEE-------------EEE-SSSTT-S-SS
T ss_pred ceehHHHHhhcCHHHHHHHHHh-hHHHH----HHhHHHHHHhccCCccce-------------eeceeccccccEee
Confidence 4455677788999888764433 00000 000123457789999997 57799999999764
No 64
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=20.04 E-value=36 Score=35.05 Aligned_cols=15 Identities=7% Similarity=-0.122 Sum_probs=13.3
Q ss_pred eeeeeccCcccchhh
Q 013256 416 FSSLNCYNLLQDLGF 430 (447)
Q Consensus 416 y~CEICGN~~Y~Gr~ 430 (447)
-.|.=||+++|+|.|
T Consensus 41 i~C~~C~~~I~kG~r 55 (324)
T PF04502_consen 41 IWCNTCGEYIYKGVR 55 (324)
T ss_pred CcCCCCcccccccee
Confidence 469999999999975
No 65
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=20.02 E-value=41 Score=38.86 Aligned_cols=18 Identities=22% Similarity=0.312 Sum_probs=16.6
Q ss_pred HHHHhcCCceeeeeeccC
Q 013256 406 LYKLHGLGQVFSSLNCYN 423 (447)
Q Consensus 406 LYKLhGL~~ey~CEICGN 423 (447)
=|+-|+=-..|||-|||-
T Consensus 624 HyrtHtGERPFkCKiCgR 641 (958)
T KOG1074|consen 624 HYRTHTGERPFKCKICGR 641 (958)
T ss_pred hhhcccCcCccccccccc
Confidence 489999999999999995
Done!