Query 029576
Match_columns 191
No_of_seqs 128 out of 236
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 15:07:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029576.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029576hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04570 DUF581: Protein of un 99.9 2.7E-26 5.8E-31 162.0 5.1 53 83-144 6-58 (58)
2 PF12855 Ecl1: Life-span regul 94.9 0.014 3E-07 39.4 1.5 31 91-136 4-34 (43)
3 PF09889 DUF2116: Uncharacteri 93.2 0.11 2.3E-06 37.2 3.2 30 94-141 4-33 (59)
4 PF06467 zf-FCS: MYM-type Zinc 91.4 0.15 3.3E-06 32.1 1.9 34 94-135 7-42 (43)
5 COG4068 Uncharacterized protei 90.4 0.24 5.3E-06 36.4 2.5 32 94-145 9-40 (64)
6 COG2075 RPL24A Ribosomal prote 87.7 0.51 1.1E-05 34.9 2.6 32 94-134 4-38 (66)
7 PRK00418 DNA gyrase inhibitor; 80.3 1 2.2E-05 32.7 1.4 36 93-143 6-41 (62)
8 PF03884 DUF329: Domain of unk 78.4 0.54 1.2E-05 33.5 -0.5 33 95-142 4-36 (57)
9 PRK01343 zinc-binding protein; 69.9 3.3 7.2E-05 29.7 1.8 31 94-143 10-40 (57)
10 smart00746 TRASH metallochaper 69.1 6.3 0.00014 21.4 2.5 34 96-136 1-35 (39)
11 PF04640 PLATZ: PLATZ transcri 68.3 2.4 5.1E-05 31.5 0.8 23 92-132 48-70 (72)
12 PRK00807 50S ribosomal protein 66.4 8 0.00017 26.7 3.1 34 94-136 2-38 (52)
13 PRK14891 50S ribosomal protein 64.0 7.2 0.00016 32.2 2.9 35 94-137 5-42 (131)
14 PF04945 YHS: YHS domain; Int 58.7 6 0.00013 25.8 1.3 32 97-138 4-38 (47)
15 COG3024 Uncharacterized protei 50.8 7.7 0.00017 28.7 0.9 36 93-143 7-42 (65)
16 PF00412 LIM: LIM domain; Int 48.8 14 0.00031 23.8 1.9 27 91-130 26-52 (58)
17 cd00472 Ribosomal_L24e_L24 Rib 46.1 26 0.00056 24.6 2.9 35 94-137 4-41 (54)
18 PF02069 Metallothio_Pro: Prok 36.2 26 0.00057 24.7 1.7 32 94-136 8-39 (52)
19 PF10367 Vps39_2: Vacuolar sor 31.1 37 0.0008 24.1 1.9 19 94-113 79-97 (109)
20 PF06906 DUF1272: Protein of u 31.0 41 0.00088 24.5 2.0 30 95-134 7-37 (57)
21 PF04181 RPAP2_Rtr1: Rtr1/RPAP 30.7 65 0.0014 23.1 3.1 52 87-138 14-72 (79)
22 PF12156 ATPase-cat_bd: Putati 30.3 1.1E+02 0.0024 22.6 4.4 44 95-145 2-46 (88)
23 PHA03073 late transcription fa 26.5 43 0.00092 28.4 1.7 38 93-136 49-86 (150)
24 PF08600 Rsm1: Rsm1-like; Int 24.4 29 0.00063 25.9 0.3 17 93-113 19-35 (91)
25 PF14453 ThiS-like: ThiS-like 24.2 38 0.00083 24.1 0.9 29 100-128 22-53 (57)
26 PF01246 Ribosomal_L24e: Ribos 24.1 82 0.0018 23.3 2.6 34 94-136 4-40 (71)
27 smart00132 LIM Zinc-binding do 22.6 96 0.0021 17.8 2.3 18 95-113 1-18 (39)
28 PF11809 DUF3330: Domain of un 21.4 65 0.0014 24.3 1.7 40 94-140 12-51 (70)
No 1
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=99.93 E-value=2.7e-26 Score=161.96 Aligned_cols=53 Identities=57% Similarity=1.049 Sum_probs=48.9
Q ss_pred CCCCCCchhHhhccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHHHHHHHHHHh
Q 029576 83 SADFLETPHFLRTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQQMNQDERKQ 144 (191)
Q Consensus 83 s~~~~e~~~FL~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~qm~~DE~~E 144 (191)
.....++.+||++|++|||+|.+++|||||| ||+||||.|||++||++||++|
T Consensus 6 ~~~~~~~~~FL~~C~~C~k~L~~~~DiymYr---------Gd~aFCS~ECR~~qi~~de~~E 58 (58)
T PF04570_consen 6 DGSPFPSEHFLSFCYLCKKKLDPGKDIYMYR---------GDKAFCSEECRSQQILMDEEKE 58 (58)
T ss_pred cCCCCCcHHHHHHHHccCCCCCCCCCeeeec---------cccccccHHHHHHHHHHHHhcC
Confidence 3444578899999999999999999999999 9999999999999999999876
No 2
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=94.94 E-value=0.014 Score=39.40 Aligned_cols=31 Identities=32% Similarity=0.746 Sum_probs=25.8
Q ss_pred hHhhccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHHH
Q 029576 91 HFLRTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQQ 136 (191)
Q Consensus 91 ~FL~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~q 136 (191)
.|+.+|-.|-|.+.... .+..|||++||.+.
T Consensus 4 ~F~~yC~~Cdk~~~~~~---------------~~~lYCSe~Cr~~D 34 (43)
T PF12855_consen 4 AFNDYCIVCDKQIDPPD---------------DGSLYCSEECRLKD 34 (43)
T ss_pred hhhhHHHHhhccccCCC---------------CCccccCHHHHhHh
Confidence 69999999999995533 47889999999764
No 3
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=93.17 E-value=0.11 Score=37.23 Aligned_cols=30 Identities=27% Similarity=0.799 Sum_probs=23.0
Q ss_pred hccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHHHHHHHH
Q 029576 94 RTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQQMNQDE 141 (191)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~qm~~DE 141 (191)
+.|-.|.+.+. -|..|||.+||+.....-+
T Consensus 4 kHC~~CG~~Ip------------------~~~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 4 KHCPVCGKPIP------------------PDESFCSPKCREEYRKRQK 33 (59)
T ss_pred CcCCcCCCcCC------------------cchhhhCHHHHHHHHHHHH
Confidence 45999999995 2689999999987654433
No 4
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=91.36 E-value=0.15 Score=32.13 Aligned_cols=34 Identities=26% Similarity=0.562 Sum_probs=21.2
Q ss_pred hccccCcCCCCCCCc--eEEEecchhhhhccCCccccChHHHHH
Q 029576 94 RTCGLCKRRLVPGRD--IYMYRLFLLMCFCRGDSAFCSLECRQQ 135 (191)
Q Consensus 94 ~~C~lCkK~L~~gkD--IYMYR~~l~~~~~~GekAFCS~ECR~~ 135 (191)
..|..|++.+....+ +..|. +-.+-|||..|+..
T Consensus 7 ~~C~~C~~~~~~~~~~~~~~~~--------g~~~~FCS~~C~~~ 42 (43)
T PF06467_consen 7 KTCSYCKKYIPNKPTMIEVQYD--------GKMKQFCSQSCLSS 42 (43)
T ss_dssp EE-TTT--EEECCC----EE-T--------TTTSCCSSHHHHHH
T ss_pred CcCcccCCcccCCCcccccccc--------CcccChhCHHHHhh
Confidence 569999999955555 56666 24678999999874
No 5
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=90.39 E-value=0.24 Score=36.41 Aligned_cols=32 Identities=38% Similarity=0.856 Sum_probs=24.4
Q ss_pred hccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHHHHHHHHHHhh
Q 029576 94 RTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQQMNQDERKQK 145 (191)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~qm~~DE~~Ek 145 (191)
+.|--|.+.+.+ |.-|||+||+ +|+..|++-+
T Consensus 9 ~HC~VCg~aIp~------------------de~~CSe~C~--eil~ker~R~ 40 (64)
T COG4068 9 RHCVVCGKAIPP------------------DEQVCSEECG--EILNKERKRQ 40 (64)
T ss_pred ccccccCCcCCC------------------ccchHHHHHH--HHHHHHHHHH
Confidence 349999999964 4569999997 5777777644
No 6
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=87.73 E-value=0.51 Score=34.93 Aligned_cols=32 Identities=38% Similarity=0.988 Sum_probs=27.3
Q ss_pred hccccCcCCCCCCCceEEEecchhhhhccCCcc---ccChHHHH
Q 029576 94 RTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSA---FCSLECRQ 134 (191)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekA---FCS~ECR~ 134 (191)
..|+.|.+.|.||.-|+--| .|.. |||..|+.
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr---------~Dg~v~~FcssKc~k 38 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVR---------NDGKVLRFCSSKCEK 38 (66)
T ss_pred eEecCcCCccCCCceEEEEe---------cCCeEEEEechhHHH
Confidence 46999999999999887667 6653 99999987
No 7
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=80.27 E-value=1 Score=32.74 Aligned_cols=36 Identities=25% Similarity=0.562 Sum_probs=23.8
Q ss_pred hhccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHHHHHHHHHH
Q 029576 93 LRTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQQMNQDERK 143 (191)
Q Consensus 93 L~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~qm~~DE~~ 143 (191)
...|-.|+|... +..-.-|| +|||..|+. |.+-+..
T Consensus 6 ~v~CP~C~k~~~-w~~~~~~r------------PFCS~RCk~--IDLg~W~ 41 (62)
T PRK00418 6 TVNCPTCGKPVE-WGEISPFR------------PFCSKRCQL--IDLGEWA 41 (62)
T ss_pred cccCCCCCCccc-ccCCCCcC------------CcccHHHHh--hhHHHHH
Confidence 456999999873 22223344 899999974 5555544
No 8
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=78.36 E-value=0.54 Score=33.50 Aligned_cols=33 Identities=18% Similarity=0.415 Sum_probs=17.0
Q ss_pred ccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHHHHHHHHH
Q 029576 95 TCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQQMNQDER 142 (191)
Q Consensus 95 ~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~qm~~DE~ 142 (191)
.|-.|+|.... .+-.= -.+|||..|| .|.+-..
T Consensus 4 ~CP~C~k~~~~-~~~n~------------~rPFCS~RCk--~iDLg~W 36 (57)
T PF03884_consen 4 KCPICGKPVEW-SPENP------------FRPFCSERCK--LIDLGRW 36 (57)
T ss_dssp E-TTT--EEE--SSSSS--------------SSSSHHHH--HHHHS-S
T ss_pred cCCCCCCeecc-cCCCC------------cCCcccHhhc--ccCHHHH
Confidence 58889988743 22222 3599999998 4554443
No 9
>PRK01343 zinc-binding protein; Provisional
Probab=69.91 E-value=3.3 Score=29.72 Aligned_cols=31 Identities=26% Similarity=0.601 Sum_probs=21.6
Q ss_pred hccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHHHHHHHHHH
Q 029576 94 RTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQQMNQDERK 143 (191)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~qm~~DE~~ 143 (191)
..|-.|+|.... -...|||..||. |.+-...
T Consensus 10 ~~CP~C~k~~~~-----------------~~rPFCS~RC~~--iDLg~W~ 40 (57)
T PRK01343 10 RPCPECGKPSTR-----------------EAYPFCSERCRD--IDLNRWL 40 (57)
T ss_pred CcCCCCCCcCcC-----------------CCCcccCHHHhh--hhHHHHh
Confidence 569999998631 135899999985 5544443
No 10
>smart00746 TRASH metallochaperone-like domain.
Probab=69.15 E-value=6.3 Score=21.36 Aligned_cols=34 Identities=24% Similarity=0.449 Sum_probs=19.7
Q ss_pred cccCcCCCCCCCceEEEecchhhhhccC-CccccChHHHHHH
Q 029576 96 CGLCKRRLVPGRDIYMYRLFLLMCFCRG-DSAFCSLECRQQQ 136 (191)
Q Consensus 96 C~lCkK~L~~gkDIYMYR~~l~~~~~~G-ekAFCS~ECR~~q 136 (191)
|..|+..+.....-.+++ ..| ..-|||.+|....
T Consensus 1 c~~C~~~~~~~~~~~~~~-------~~g~~~~FCs~~c~~~~ 35 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVV-------NDGKVFYFCSSKCLSKF 35 (39)
T ss_pred CCCCCCCccCCCCceEEE-------ECCEEEEEeCHHHHHHH
Confidence 677888885222222222 002 3469999998754
No 11
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=68.34 E-value=2.4 Score=31.48 Aligned_cols=23 Identities=52% Similarity=1.042 Sum_probs=18.4
Q ss_pred HhhccccCcCCCCCCCceEEEecchhhhhccCCccccChHH
Q 029576 92 FLRTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLEC 132 (191)
Q Consensus 92 FL~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~EC 132 (191)
.-..|..|.+.|. |- |+ |||..|
T Consensus 48 ~~~~C~~C~R~L~---d~--~~-------------fCSl~C 70 (72)
T PF04640_consen 48 SGNICETCHRSLQ---DP--YR-------------FCSLSC 70 (72)
T ss_pred CCCccCCCCCCCC---CC--Ce-------------EEeeeE
Confidence 6678999999994 42 55 899888
No 12
>PRK00807 50S ribosomal protein L24e; Validated
Probab=66.37 E-value=8 Score=26.67 Aligned_cols=34 Identities=32% Similarity=0.810 Sum_probs=26.4
Q ss_pred hccccCcCCCCCCCceEEEecchhhhhccCCc---cccChHHHHHH
Q 029576 94 RTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDS---AFCSLECRQQQ 136 (191)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR~~l~~~~~~Gek---AFCS~ECR~~q 136 (191)
..|..|...+.||.-+..+| .|. -|||..|....
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr---------~Dgkv~~Fcs~KC~~~f 38 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVK---------KDGTILYFCSSKCEKNY 38 (52)
T ss_pred cccCCCCCeEcCCCCeEEEE---------eCCcEEEEeCHHHHHHH
Confidence 46999999999888877666 333 59999997644
No 13
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=64.03 E-value=7.2 Score=32.24 Aligned_cols=35 Identities=26% Similarity=0.540 Sum_probs=25.9
Q ss_pred hccccCcCCCCCCCceEEEecchhhhhccCCc---cccChHHHHHHH
Q 029576 94 RTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDS---AFCSLECRQQQM 137 (191)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR~~l~~~~~~Gek---AFCS~ECR~~qm 137 (191)
..|++|..+|-||.-|-.-| .|. -|||..|....+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR---------~DGkvf~FcssKC~k~f~ 42 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVR---------KDGTVLHFVDSKCEKNYD 42 (131)
T ss_pred eeecCcCCcccCCCCcEEEe---------cCCCEEEEecHHHHHHHH
Confidence 46999999999998664445 443 499999965443
No 14
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=58.65 E-value=6 Score=25.76 Aligned_cols=32 Identities=28% Similarity=0.617 Sum_probs=19.0
Q ss_pred ccCcCCCCCC--CceEEEecchhhhhccCC-ccccChHHHHHHHH
Q 029576 97 GLCKRRLVPG--RDIYMYRLFLLMCFCRGD-SAFCSLECRQQQMN 138 (191)
Q Consensus 97 ~lCkK~L~~g--kDIYMYR~~l~~~~~~Ge-kAFCS~ECR~~qm~ 138 (191)
.-|...| ++ ...+.|+ |. --|||.+|+..-..
T Consensus 4 Pvcg~~v-~~~~~~~~~y~---------G~~Y~FCS~~C~~~F~~ 38 (47)
T PF04945_consen 4 PVCGMKV-PGNAAYSVEYN---------GRTYYFCSEGCKEKFEA 38 (47)
T ss_dssp -GGG-BE------EEEEET---------TEEEEESSHHHHHHHHC
T ss_pred CCCCCEE-ccCccEEEEEC---------CEEEEEcCHHHHHHHHH
Confidence 3477777 43 3556666 54 47999999986543
No 15
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.84 E-value=7.7 Score=28.75 Aligned_cols=36 Identities=22% Similarity=0.508 Sum_probs=25.2
Q ss_pred hhccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHHHHHHHHHH
Q 029576 93 LRTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQQMNQDERK 143 (191)
Q Consensus 93 L~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~qm~~DE~~ 143 (191)
-.-|-.|.|.. .+.++-=|| +|||..|. .|.+-+..
T Consensus 7 ~v~CP~Cgkpv-~w~~~s~fr------------PFCSkRCk--lIDLg~Wa 42 (65)
T COG3024 7 TVPCPTCGKPV-VWGEESPFR------------PFCSKRCK--LIDLGEWA 42 (65)
T ss_pred cccCCCCCCcc-cccccCCcC------------cchhHhhh--hcchhhhh
Confidence 34699999998 444544455 89999885 56666654
No 16
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=48.84 E-value=14 Score=23.76 Aligned_cols=27 Identities=22% Similarity=0.632 Sum_probs=18.8
Q ss_pred hHhhccccCcCCCCCCCceEEEecchhhhhccCCccccCh
Q 029576 91 HFLRTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSL 130 (191)
Q Consensus 91 ~FL~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ 130 (191)
.|- |..|++.|.++. |... ..+.||..
T Consensus 26 Cf~--C~~C~~~l~~~~--~~~~---------~~~~~C~~ 52 (58)
T PF00412_consen 26 CFK--CSKCGKPLNDGD--FYEK---------DGKPYCKD 52 (58)
T ss_dssp TSB--ETTTTCBTTTSS--EEEE---------TTEEEEHH
T ss_pred ccc--cCCCCCccCCCe--eEeE---------CCEEECHH
Confidence 454 999999996554 4444 46888864
No 17
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=46.08 E-value=26 Score=24.61 Aligned_cols=35 Identities=29% Similarity=0.785 Sum_probs=27.0
Q ss_pred hccccCcCCCCCCCceEEEecchhhhhccCCc---cccChHHHHHHH
Q 029576 94 RTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDS---AFCSLECRQQQM 137 (191)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR~~l~~~~~~Gek---AFCS~ECR~~qm 137 (191)
..|..|..+|-||.-+-.-| .|. -|||..|+...+
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr---------~Dgkv~~F~s~Kc~~~~~ 41 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVR---------NDGKVFRFCSSKCEKNFL 41 (54)
T ss_pred EEecCcCCeecCCCccEEEe---------cCCCEEEEECHHHHHHHH
Confidence 46999999999998766556 554 499999976543
No 18
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=36.18 E-value=26 Score=24.75 Aligned_cols=32 Identities=16% Similarity=0.419 Sum_probs=17.2
Q ss_pred hccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHHH
Q 029576 94 RTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQQ 136 (191)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~q 136 (191)
-.|..|+=-+..... ++ + .-+.|||.+|-..+
T Consensus 8 CaC~~C~C~V~~~~A-i~-~---------dGk~YCS~aCA~gH 39 (52)
T PF02069_consen 8 CACPSCSCVVSEEEA-IQ-K---------DGKYYCSEACANGH 39 (52)
T ss_dssp -SSTT----B-TTTS-EE-S---------SS-EESSHHHHHTS
T ss_pred ecCCCCEeEECchHh-HH-h---------CCEeeecHHHhccC
Confidence 357778877755433 33 3 57999999997655
No 19
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=31.09 E-value=37 Score=24.05 Aligned_cols=19 Identities=16% Similarity=0.496 Sum_probs=15.0
Q ss_pred hccccCcCCCCCCCceEEEe
Q 029576 94 RTCGLCKRRLVPGRDIYMYR 113 (191)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR 113 (191)
..|..|+|+|+. ..+++|-
T Consensus 79 ~~C~vC~k~l~~-~~f~~~p 97 (109)
T PF10367_consen 79 TKCSVCGKPLGN-SVFVVFP 97 (109)
T ss_pred CCccCcCCcCCC-ceEEEeC
Confidence 459999999965 6777775
No 20
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=30.96 E-value=41 Score=24.46 Aligned_cols=30 Identities=27% Similarity=0.871 Sum_probs=24.4
Q ss_pred ccccCcCCCCCCC-ceEEEecchhhhhccCCccccChHHHH
Q 029576 95 TCGLCKRRLVPGR-DIYMYRLFLLMCFCRGDSAFCSLECRQ 134 (191)
Q Consensus 95 ~C~lCkK~L~~gk-DIYMYR~~l~~~~~~GekAFCS~ECR~ 134 (191)
.|-.|.+.|.++. |.||.. .|=-||. +|-+
T Consensus 7 nCE~C~~dLp~~s~~A~ICS---------fECTFC~-~C~e 37 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICS---------FECTFCA-DCAE 37 (57)
T ss_pred CccccCCCCCCCCCcceEEe---------EeCcccH-HHHH
Confidence 5889999998888 899988 8888885 4543
No 21
>PF04181 RPAP2_Rtr1: Rtr1/RPAP2 family; InterPro: IPR007308 This entry represents a domain found in PAP2 (RNAP II associated polypeptide) protein and the yeast Rtr1 proteins. Its function is not known however it is thought to be a zinc finger.
Probab=30.65 E-value=65 Score=23.11 Aligned_cols=52 Identities=25% Similarity=0.337 Sum_probs=27.7
Q ss_pred CCchhHhhccc--cCcCCCCCCCceEEEecchh---hhhcc--CCccccChHHHHHHHH
Q 029576 87 LETPHFLRTCG--LCKRRLVPGRDIYMYRLFLL---MCFCR--GDSAFCSLECRQQQMN 138 (191)
Q Consensus 87 ~e~~~FL~~C~--lCkK~L~~gkDIYMYR~~l~---~~~~~--GekAFCS~ECR~~qm~ 138 (191)
.+..+....|. +|.+.+......=.|++.+. +.-.. -...|||..|...-..
T Consensus 14 v~ER~~~~~CGYplC~~~~~~~~~~~~y~i~~~~~~v~~~~~~~~~~fCS~~C~~~s~~ 72 (79)
T PF04181_consen 14 VEERNINGLCGYPLCSNPPPKISSRQKYRIDLKANKVYDITERELSKFCSKDCYKASEF 72 (79)
T ss_pred HHHHHhCCCCCCccCCCCcccccCCCCeEEECCCCeecccccChhcCcCCHHHHHHHHH
Confidence 34445566675 68888866622223342211 11111 1138999999876443
No 22
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=30.31 E-value=1.1e+02 Score=22.65 Aligned_cols=44 Identities=18% Similarity=0.368 Sum_probs=32.3
Q ss_pred ccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHH-HHHHHHHHhh
Q 029576 95 TCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQ-QMNQDERKQK 145 (191)
Q Consensus 95 ~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~-qm~~DE~~Ek 145 (191)
.|+.|...+..+..|-+.- -..++.||..-|..- +|+.+...+.
T Consensus 2 ~C~HCg~~~p~~~~~~~~~-------~g~~~~FCC~GC~~V~~~i~~~gL~~ 46 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEI-------DGEERPFCCPGCQAVYQLIHENGLES 46 (88)
T ss_pred CCCCCCCCCCCCCCeeeee-------CCCccccccHHHHHHHHHHHHcchHH
Confidence 5999999997676666554 113689999999865 4666766665
No 23
>PHA03073 late transcription factor VLTF-2; Provisional
Probab=26.46 E-value=43 Score=28.38 Aligned_cols=38 Identities=26% Similarity=0.493 Sum_probs=25.1
Q ss_pred hhccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHHH
Q 029576 93 LRTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQQ 136 (191)
Q Consensus 93 L~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~q 136 (191)
-..|-.|+..|... ++++=-| .-.--..|||.=||+--
T Consensus 49 ~~~CwfC~q~~~~~-~~~iETl-----~g~~vg~FCS~ICRDSf 86 (150)
T PHA03073 49 NDYCWFCKQDLIIA-PLFIETL-----KGGAVGYFCSKICRDSF 86 (150)
T ss_pred CCcEEeeccccccC-ceEEEee-----cCchhhhHhHHHHHHHH
Confidence 35699999999654 4654331 11123579999999854
No 24
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=24.36 E-value=29 Score=25.93 Aligned_cols=17 Identities=41% Similarity=1.028 Sum_probs=15.5
Q ss_pred hhccccCcCCCCCCCceEEEe
Q 029576 93 LRTCGLCKRRLVPGRDIYMYR 113 (191)
Q Consensus 93 L~~C~lCkK~L~~gkDIYMYR 113 (191)
|-.|..|.|+|+ ++||+
T Consensus 19 ~~~C~~C~Rr~G----LW~f~ 35 (91)
T PF08600_consen 19 LLSCSYCFRRLG----LWMFK 35 (91)
T ss_pred eEEccccCcEee----eeecc
Confidence 778999999995 89998
No 25
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=24.24 E-value=38 Score=24.14 Aligned_cols=29 Identities=24% Similarity=0.363 Sum_probs=21.6
Q ss_pred cCCCCCCCceEEEecc---hhhhhccCCcccc
Q 029576 100 KRRLVPGRDIYMYRLF---LLMCFCRGDSAFC 128 (191)
Q Consensus 100 kK~L~~gkDIYMYR~~---l~~~~~~GekAFC 128 (191)
++.+.++.||++|-+| -=+.+.+||.-||
T Consensus 22 r~~~k~~~DI~I~NGF~~~~d~~L~e~D~v~~ 53 (57)
T PF14453_consen 22 RKESKPDADIVILNGFPTKEDIELKEGDEVFL 53 (57)
T ss_pred HHhhCCCCCEEEEcCcccCCccccCCCCEEEE
Confidence 4578889999999987 3355666776665
No 26
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=24.14 E-value=82 Score=23.26 Aligned_cols=34 Identities=26% Similarity=0.631 Sum_probs=22.3
Q ss_pred hccccCcCCCCCCCceEEEecchhhhhccCCc---cccChHHHHHH
Q 029576 94 RTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDS---AFCSLECRQQQ 136 (191)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR~~l~~~~~~Gek---AFCS~ECR~~q 136 (191)
..|..|...|-||.-+..-| -|. -|||.-|+...
T Consensus 4 ~~C~Fsg~~I~PG~G~~~Vr---------~DG~v~~F~s~Kc~~~~ 40 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHGKMYVR---------NDGKVFYFCSSKCEKLF 40 (71)
T ss_dssp EE-TTT-SEE-SSSSEEEE----------TTS-EEEESSHHHHHHH
T ss_pred EEecccCCccCCCCCeEEEe---------cCCCeEEEeCHHHHHHH
Confidence 46999999999998765444 332 49999998654
No 27
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=22.60 E-value=96 Score=17.79 Aligned_cols=18 Identities=17% Similarity=0.565 Sum_probs=12.1
Q ss_pred ccccCcCCCCCCCceEEEe
Q 029576 95 TCGLCKRRLVPGRDIYMYR 113 (191)
Q Consensus 95 ~C~lCkK~L~~gkDIYMYR 113 (191)
.|..|++.|.++ +.++..
T Consensus 1 ~C~~C~~~i~~~-~~~~~~ 18 (39)
T smart00132 1 KCAGCGKPIRGG-ELVLRA 18 (39)
T ss_pred CccccCCcccCC-cEEEEe
Confidence 488999999655 344433
No 28
>PF11809 DUF3330: Domain of unknown function (DUF3330); InterPro: IPR021767 This family of proteins are functionally uncharacterised. This family is only found in bacteria.
Probab=21.43 E-value=65 Score=24.30 Aligned_cols=40 Identities=20% Similarity=0.437 Sum_probs=21.4
Q ss_pred hccccCcCCCCCCCceEEEecchhhhhccCCccccChHHHHHHHHHH
Q 029576 94 RTCGLCKRRLVPGRDIYMYRLFLLMCFCRGDSAFCSLECRQQQMNQD 140 (191)
Q Consensus 94 ~~C~lCkK~L~~gkDIYMYR~~l~~~~~~GekAFCS~ECR~~qm~~D 140 (191)
..|..|.|.|.... .+.-- -...-.-||..||-++-....
T Consensus 12 ~sC~vC~KEIPl~~-a~t~E------~~eYV~hFCGLeCY~~w~a~~ 51 (70)
T PF11809_consen 12 TSCCVCCKEIPLDA-AFTPE------AAEYVEHFCGLECYQRWQARA 51 (70)
T ss_pred chHHHHhhhCChhh-ccCcc------hHHHHHHHhhHHHHHHHHHHH
Confidence 35888888884322 11111 000124599999976655333
Done!