Query 019559
Match_columns 339
No_of_seqs 135 out of 158
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 02:43:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019559.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019559hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00612 IQ: IQ calmodulin-bin 96.2 0.0036 7.9E-08 38.3 1.9 20 111-130 1-20 (21)
2 smart00015 IQ Short calmodulin 95.4 0.011 2.4E-07 37.7 2.0 21 110-130 2-22 (26)
3 TIGR03300 assembly_YfgL outer 63.1 22 0.00047 33.8 6.4 82 257-338 283-375 (377)
4 PF08763 Ca_chan_IQ: Voltage g 60.4 6.6 0.00014 28.0 1.8 20 111-130 9-28 (35)
5 PRK11138 outer membrane biogen 57.3 25 0.00055 34.0 5.8 111 227-338 266-390 (394)
6 KOG0377 Protein serine/threoni 50.6 9.1 0.0002 40.7 1.7 22 111-132 17-38 (631)
7 PF13360 PQQ_2: PQQ-like domai 50.4 42 0.00091 28.9 5.5 44 272-315 12-61 (238)
8 PF13570 PQQ_3: PQQ-like domai 49.4 25 0.00053 23.7 3.2 32 273-304 1-35 (40)
9 KOG4427 E3 ubiquitin protein l 40.2 15 0.00032 41.3 1.5 24 109-132 28-51 (1096)
10 PF10411 DsbC_N: Disulfide bon 40.0 49 0.0011 24.6 3.8 27 265-303 25-51 (57)
11 PRK11138 outer membrane biogen 39.4 68 0.0015 31.1 5.7 82 256-337 259-348 (394)
12 KOG0942 E3 ubiquitin protein l 38.7 15 0.00032 41.6 1.2 22 109-130 27-48 (1001)
13 KOG3556 Familial cylindromatos 26.6 68 0.0015 35.0 3.6 70 228-299 232-311 (724)
14 PF13360 PQQ_2: PQQ-like domai 26.6 1.6E+02 0.0035 25.3 5.4 61 256-316 39-102 (238)
15 cd05727 Ig2_Contactin-2-like S 25.9 1.4E+02 0.003 24.7 4.6 34 274-308 35-68 (96)
16 TIGR03300 assembly_YfgL outer 25.0 1.9E+02 0.0041 27.5 6.0 48 265-312 77-127 (377)
17 PF13509 S1_2: S1 domain; PDB: 24.9 56 0.0012 24.5 2.0 34 226-270 13-48 (61)
18 TIGR02658 TTQ_MADH_Hv methylam 23.5 90 0.002 31.4 3.7 70 226-306 127-221 (352)
19 PF00727 IL4: Interleukin 4 Th 21.4 94 0.002 27.3 2.9 28 97-124 29-59 (117)
20 COG4382 Mu-like prophage prote 21.0 1.4E+02 0.003 27.9 4.1 65 145-220 75-139 (170)
21 COG4632 EpsL Exopolysaccharide 20.7 1.4E+02 0.003 30.2 4.2 63 267-335 156-220 (320)
No 1
>PF00612 IQ: IQ calmodulin-binding motif; InterPro: IPR000048 The IQ motif is an extremely basic unit of about 23 amino acids, whose conserved core usually fits the consensus A-x(3)-I-Q-x(2)-F-R-x(4)-K-K. The IQ motif, which can be present in one or more copies, serves as a binding site for different EF-hand proteins including the essential and regulatory myosin light chains, calmodulin (CaM), and CaM-like proteins [, ].Many IQ motifs are protein kinase C (PKC) phosphorylation sites [, ]. Resolution of the 3D structure of scallop myosin has shown that the IQ motif forms a basic amphipathic helix []. Some proteins known to contain an IQ motif are listed below: A number of conventional and unconventional myosins. Neuromodulin (GAP-43). This protein is associated with nerve growth. It is a major component of the motile "growth cones" that form the tips of elongating axons. Neurogranin (NG/p17). Acts as a "third messenger" substrate of protein kinase C-mediated molecular cascades during synaptic development and remodeling. Sperm surface protein Sp17. Ras GTPase-activating-like protein IQGAP1. IQGAP1 contains 4 IQ motifs. This entry covers the entire IQ motif.; GO: 0005515 protein binding; PDB: 2DFS_A 2IX7_C 1OE9_A 1W7J_A 1W7I_A 1KQM_A 1KK7_A 1WDC_A 1DFL_A 1B7T_A ....
Probab=96.15 E-value=0.0036 Score=38.28 Aligned_cols=20 Identities=25% Similarity=0.451 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhhhhhhhhcc
Q 019559 111 DAAATKLQKVYKSYRTRRNL 130 (339)
Q Consensus 111 ~~AA~~IQKvYRgYRTRR~L 130 (339)
..||++||+.||||..|+++
T Consensus 1 ~~aai~iQ~~~R~~~~Rk~~ 20 (21)
T PF00612_consen 1 RKAAIIIQSYWRGYLARKRY 20 (21)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHhc
Confidence 37999999999999999875
No 2
>smart00015 IQ Short calmodulin-binding motif containing conserved Ile and Gln residues. Calmodulin-binding motif.
Probab=95.43 E-value=0.011 Score=37.66 Aligned_cols=21 Identities=29% Similarity=0.506 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHhhhhhhhhcc
Q 019559 110 LDAAATKLQKVYKSYRTRRNL 130 (339)
Q Consensus 110 ~~~AA~~IQKvYRgYRTRR~L 130 (339)
...||++||..||||..|++.
T Consensus 2 ~~~aa~~IQa~~Rg~~~r~~y 22 (26)
T smart00015 2 LTRAAIIIQAAWRGYLARKRY 22 (26)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 468999999999999999986
No 3
>TIGR03300 assembly_YfgL outer membrane assembly lipoprotein YfgL. Members of this protein family are YfgL, a lipoprotein component of a complex that acts protein insertion into the bacterial outer membrane. Other members of this complex are NlpB, YfiO, and YaeT. This protein contains multiple copies of a repeat that, in other contexts, are associated with binding of the coenzyme PQQ.
Probab=63.13 E-value=22 Score=33.81 Aligned_cols=82 Identities=15% Similarity=0.124 Sum_probs=47.8
Q ss_pred cCChhhhcceEEEEecCeEEEcccC--ceeeccC--CCeEEEEEcCCCceeeecCCCCcccccccC-----CCCccccce
Q 019559 257 YLGPKEREEFEVVVESGKLVYRQTG--MFVNTNE--DSKWIFVLSTSRALYVGQKKKGVFQHSSFL-----SGGAITAAG 327 (339)
Q Consensus 257 YL~p~ERe~YeV~VedGkL~yk~sg--~~vdT~~--~~kWIFVmdts~~LYvG~KkkG~FQHSSFL-----aGg~t~AAG 327 (339)
|.....-.-|-+...+|+++|+... ....++. .+.-|||.+.+|.||+=..++|.+.-+--+ ...++.+-|
T Consensus 283 yv~~~~G~l~~~d~~tG~~~W~~~~~~~~~~ssp~i~g~~l~~~~~~G~l~~~d~~tG~~~~~~~~~~~~~~~sp~~~~~ 362 (377)
T TIGR03300 283 YVTDADGVVVALDRRSGSELWKNDELKYRQLTAPAVVGGYLVVGDFEGYLHWLSREDGSFVARLKTDGSGIASPPVVVGD 362 (377)
T ss_pred EEECCCCeEEEEECCCCcEEEccccccCCccccCEEECCEEEEEeCCCEEEEEECCCCCEEEEEEcCCCccccCCEEECC
Confidence 3433333444444457777777632 1111111 245799999999999998888988744333 334445555
Q ss_pred eEEE--ecCeeee
Q 019559 328 RLVA--HDGILEV 338 (339)
Q Consensus 328 ~Lvv--~dG~Lka 338 (339)
.|.+ .||.|-+
T Consensus 363 ~l~v~~~dG~l~~ 375 (377)
T TIGR03300 363 GLLVQTRDGDLYA 375 (377)
T ss_pred EEEEEeCCceEEE
Confidence 5544 4676654
No 4
>PF08763 Ca_chan_IQ: Voltage gated calcium channel IQ domain; InterPro: IPR014873 Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins []. The activity of this pore is modulated by 4 tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits. Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels. The voltage-gated calcium channel alpha 1 subunit contains an IQ domain, named for its isoleucine-glutamine (IQ) motif, which interacts with hydrophobic pockets of Ca2+/calmodulin []. The interaction regulates two self-regulatory calcium dependent feedback mechanisms, calcium dependent inactivation (CDI), and calcium-dependent facilitation (CDF). ; PDB: 3OXQ_F 2F3Z_B 3G43_E 2F3Y_B 2BE6_D 3DVM_B 3BXK_D 2VAY_B 3DVK_B 3BXL_B ....
Probab=60.37 E-value=6.6 Score=27.97 Aligned_cols=20 Identities=15% Similarity=0.341 Sum_probs=17.3
Q ss_pred HHHHHHHHHHhhhhhhhhcc
Q 019559 111 DAAATKLQKVYKSYRTRRNL 130 (339)
Q Consensus 111 ~~AA~~IQKvYRgYRTRR~L 130 (339)
-=||..||..||.++.||+-
T Consensus 9 ~YAt~lI~dyfr~~K~rk~~ 28 (35)
T PF08763_consen 9 FYATLLIQDYFRQFKKRKEQ 28 (35)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 35899999999999999863
No 5
>PRK11138 outer membrane biogenesis protein BamB; Provisional
Probab=57.33 E-value=25 Score=33.98 Aligned_cols=111 Identities=15% Similarity=0.168 Sum_probs=63.9
Q ss_pred CceEEeecCCCCcc---CCCCCCcccccccccccCChhhhcceEEEEecCeEEEcccC--ceeeccC--CCeEEEEEcCC
Q 019559 227 PFFYWLDVGDGKEV---NLEKCPRNVLQRQCIKYLGPKEREEFEVVVESGKLVYRQTG--MFVNTNE--DSKWIFVLSTS 299 (339)
Q Consensus 227 ~FFyWLD~G~Gk~v---~le~CpR~kL~~q~V~YL~p~ERe~YeV~VedGkL~yk~sg--~~vdT~~--~~kWIFVmdts 299 (339)
.-+|-||.-.|+.+ ++..... -....-.-|+.-..-.-|-+..++|+++|.++. ....++. .+.-|||.+.+
T Consensus 266 g~l~ald~~tG~~~W~~~~~~~~~-~~~~~~~vy~~~~~g~l~ald~~tG~~~W~~~~~~~~~~~sp~v~~g~l~v~~~~ 344 (394)
T PRK11138 266 GNLVALDLRSGQIVWKREYGSVND-FAVDGGRIYLVDQNDRVYALDTRGGVELWSQSDLLHRLLTAPVLYNGYLVVGDSE 344 (394)
T ss_pred CeEEEEECCCCCEEEeecCCCccC-cEEECCEEEEEcCCCeEEEEECCCCcEEEcccccCCCcccCCEEECCEEEEEeCC
Confidence 45678888888753 2222111 111122345554455555555668888887652 1222222 24568999999
Q ss_pred CceeeecCCCCcccccccCCC-----CccccceeEEE--ecCeeee
Q 019559 300 RALYVGQKKKGVFQHSSFLSG-----GAITAAGRLVA--HDGILEV 338 (339)
Q Consensus 300 ~~LYvG~KkkG~FQHSSFLaG-----g~t~AAG~Lvv--~dG~Lka 338 (339)
|.||+=..+.|.+--+.-+.+ .++.+-|+|.| .||.|-+
T Consensus 345 G~l~~ld~~tG~~~~~~~~~~~~~~s~P~~~~~~l~v~t~~G~l~~ 390 (394)
T PRK11138 345 GYLHWINREDGRFVAQQKVDSSGFLSEPVVADDKLLIQARDGTVYA 390 (394)
T ss_pred CEEEEEECCCCCEEEEEEcCCCcceeCCEEECCEEEEEeCCceEEE
Confidence 999987777888765544432 34556666665 4666654
No 6
>KOG0377 consensus Protein serine/threonine phosphatase RDGC/PPEF, contains STphosphatase and EF-hand domains [Signal transduction mechanisms]
Probab=50.61 E-value=9.1 Score=40.66 Aligned_cols=22 Identities=32% Similarity=0.371 Sum_probs=19.1
Q ss_pred HHHHHHHHHHhhhhhhhhccCC
Q 019559 111 DAAATKLQKVYKSYRTRRNLAD 132 (339)
Q Consensus 111 ~~AA~~IQKvYRgYRTRR~Lag 132 (339)
-+||+.|||-||+|-.|+++.-
T Consensus 17 ikaAilIQkWYRr~~ARle~rr 38 (631)
T KOG0377|consen 17 IKAAILIQKWYRRYEARLEARR 38 (631)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999987653
No 7
>PF13360 PQQ_2: PQQ-like domain; PDB: 3HXJ_B 1YIQ_A 1KV9_A 3Q54_A 2YH3_A 3PRW_A 3P1L_A 3Q7M_A 3Q7O_A 3Q7N_A ....
Probab=50.43 E-value=42 Score=28.95 Aligned_cols=44 Identities=25% Similarity=0.302 Sum_probs=23.4
Q ss_pred cCeEEEccc-----Cceee-ccCCCeEEEEEcCCCceeeecCCCCccccc
Q 019559 272 SGKLVYRQT-----GMFVN-TNEDSKWIFVLSTSRALYVGQKKKGVFQHS 315 (339)
Q Consensus 272 dGkL~yk~s-----g~~vd-T~~~~kWIFVmdts~~LYvG~KkkG~FQHS 315 (339)
+|+.+|... +..+. +..++..+||.+.++.||+=....|....+
T Consensus 12 tG~~~W~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~l~~~d~~tG~~~W~ 61 (238)
T PF13360_consen 12 TGKELWSYDLGPGIGGPVATAVPDGGRVYVASGDGNLYALDAKTGKVLWR 61 (238)
T ss_dssp TTEEEEEEECSSSCSSEEETEEEETTEEEEEETTSEEEEEETTTSEEEEE
T ss_pred CCCEEEEEECCCCCCCccceEEEeCCEEEEEcCCCEEEEEECCCCCEEEE
Confidence 566666552 22231 222455566666666666666666654433
No 8
>PF13570 PQQ_3: PQQ-like domain; PDB: 3HXJ_B 3Q54_A.
Probab=49.38 E-value=25 Score=23.67 Aligned_cols=32 Identities=19% Similarity=0.339 Sum_probs=16.2
Q ss_pred CeEEEccc-CceeeccC--CCeEEEEEcCCCceee
Q 019559 273 GKLVYRQT-GMFVNTNE--DSKWIFVLSTSRALYV 304 (339)
Q Consensus 273 GkL~yk~s-g~~vdT~~--~~kWIFVmdts~~LYv 304 (339)
|+++|..+ +..+.++. .+.-+||.+.+|+||+
T Consensus 1 G~~~W~~~~~~~~~~~~~v~~g~vyv~~~dg~l~a 35 (40)
T PF13570_consen 1 GKVLWSYDTGGPIWSSPAVAGGRVYVGTGDGNLYA 35 (40)
T ss_dssp S-EEEEEE-SS---S--EECTSEEEEE-TTSEEEE
T ss_pred CceeEEEECCCCcCcCCEEECCEEEEEcCCCEEEE
Confidence 56666664 22333222 2446888888888886
No 9
>KOG4427 consensus E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.18 E-value=15 Score=41.30 Aligned_cols=24 Identities=33% Similarity=0.398 Sum_probs=21.1
Q ss_pred hHHHHHHHHHHHhhhhhhhhccCC
Q 019559 109 ELDAAATKLQKVYKSYRTRRNLAD 132 (339)
Q Consensus 109 e~~~AA~~IQKvYRgYRTRR~Lag 132 (339)
..++||..||++.|||=+|+.+++
T Consensus 28 rr~~aa~~iq~~lrsyl~Rkk~~~ 51 (1096)
T KOG4427|consen 28 RREAAALFIQRVLRSYLVRKKAQI 51 (1096)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367899999999999999988764
No 10
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=39.97 E-value=49 Score=24.65 Aligned_cols=27 Identities=33% Similarity=0.797 Sum_probs=16.8
Q ss_pred ceEEEEecCeEEEcccCceeeccCCCeEEEEEcCCCcee
Q 019559 265 EFEVVVESGKLVYRQTGMFVNTNEDSKWIFVLSTSRALY 303 (339)
Q Consensus 265 ~YeV~VedGkL~yk~sg~~vdT~~~~kWIFVmdts~~LY 303 (339)
-|||.+.+|.++| ++++++++|+ |.||
T Consensus 25 lyeV~~~~~~i~Y--------~~~dg~yli~----G~l~ 51 (57)
T PF10411_consen 25 LYEVVLKGGGILY--------VDEDGRYLIQ----GQLY 51 (57)
T ss_dssp EEEEEE-TTEEEE--------EETTSSEEEE----S-EE
T ss_pred eEEEEECCCeEEE--------EcCCCCEEEE----eEEE
Confidence 5888886666555 4566777766 6665
No 11
>PRK11138 outer membrane biogenesis protein BamB; Provisional
Probab=39.35 E-value=68 Score=31.08 Aligned_cols=82 Identities=20% Similarity=0.257 Sum_probs=45.6
Q ss_pred ccCChhhhcceEEEEecCeEEEcccC-ceeeccCCCeEEEEEcCCCceeeecCCCCcccc-cccC----CCCccccceeE
Q 019559 256 KYLGPKEREEFEVVVESGKLVYRQTG-MFVNTNEDSKWIFVLSTSRALYVGQKKKGVFQH-SSFL----SGGAITAAGRL 329 (339)
Q Consensus 256 ~YL~p~ERe~YeV~VedGkL~yk~sg-~~vdT~~~~kWIFVmdts~~LYvG~KkkG~FQH-SSFL----aGg~t~AAG~L 329 (339)
-|+.-.+-.-|-+...+|+++|++.= ....-.-.+..|||.+.++.||+=..+.|...= .+-+ ..+++++-|+|
T Consensus 259 vy~~~~~g~l~ald~~tG~~~W~~~~~~~~~~~~~~~~vy~~~~~g~l~ald~~tG~~~W~~~~~~~~~~~sp~v~~g~l 338 (394)
T PRK11138 259 VYALAYNGNLVALDLRSGQIVWKREYGSVNDFAVDGGRIYLVDQNDRVYALDTRGGVELWSQSDLLHRLLTAPVLYNGYL 338 (394)
T ss_pred EEEEEcCCeEEEEECCCCCEEEeecCCCccCcEEECCEEEEEcCCCeEEEEECCCCcEEEcccccCCCcccCCEEECCEE
Confidence 34433333334444457888887641 111111235689999999999998888886431 1112 23455566666
Q ss_pred EEe--cCeee
Q 019559 330 VAH--DGILE 337 (339)
Q Consensus 330 vv~--dG~Lk 337 (339)
.+- ||.|.
T Consensus 339 ~v~~~~G~l~ 348 (394)
T PRK11138 339 VVGDSEGYLH 348 (394)
T ss_pred EEEeCCCEEE
Confidence 653 45554
No 12
>KOG0942 consensus E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.71 E-value=15 Score=41.63 Aligned_cols=22 Identities=27% Similarity=0.552 Sum_probs=19.2
Q ss_pred hHHHHHHHHHHHhhhhhhhhcc
Q 019559 109 ELDAAATKLQKVYKSYRTRRNL 130 (339)
Q Consensus 109 e~~~AA~~IQKvYRgYRTRR~L 130 (339)
.++.+|++||+-.||||.|++-
T Consensus 27 k~e~~av~vQs~~Rg~~~r~~~ 48 (1001)
T KOG0942|consen 27 KQEKNAVKVQSFWRGFRVRHNQ 48 (1001)
T ss_pred HHhccchHHHHHHHHHHHHHHH
Confidence 3678999999999999999764
No 13
>KOG3556 consensus Familial cylindromatosis protein [General function prediction only]
Probab=26.60 E-value=68 Score=35.01 Aligned_cols=70 Identities=26% Similarity=0.253 Sum_probs=48.6
Q ss_pred ceEEeecCCCCccCCCCCCcccccccccccCC-hhhhcceEEEEe-cCeE--------EEcccCceeeccCCCeEEEEEc
Q 019559 228 FFYWLDVGDGKEVNLEKCPRNVLQRQCIKYLG-PKEREEFEVVVE-SGKL--------VYRQTGMFVNTNEDSKWIFVLS 297 (339)
Q Consensus 228 FFyWLD~G~Gk~v~le~CpR~kL~~q~V~YL~-p~ERe~YeV~Ve-dGkL--------~yk~sg~~vdT~~~~kWIFVmd 297 (339)
|-.=|-+|+--+|.-++..|. .--.|++.| |-|-..-.+-|| ||.- =+..+|.++.|--+++|+|||+
T Consensus 232 ~~~~L~IGslveV~np~~~~~--~ygvVrWIG~pP~~~~Vl~gve~edet~~~~~~~~dgs~~g~Rlftc~d~~a~Fv~~ 309 (724)
T KOG3556|consen 232 FILNLKIGSLVEVENPETMRR--VYGVVRWIGEPPEASGVLYGVEFEDETSQWPSSNQDGSSSGDRLFTCFDTNANFVMS 309 (724)
T ss_pred ccccceecceEEecCCccccc--cceeeEecccCCcccCceEeeeecCccccCccccccCcccCceeeeeccccceeeEc
Confidence 334488988888887644432 135688888 446666666665 4332 2556789999999999999998
Q ss_pred CC
Q 019559 298 TS 299 (339)
Q Consensus 298 ts 299 (339)
.+
T Consensus 310 ~s 311 (724)
T KOG3556|consen 310 GS 311 (724)
T ss_pred CC
Confidence 64
No 14
>PF13360 PQQ_2: PQQ-like domain; PDB: 3HXJ_B 1YIQ_A 1KV9_A 3Q54_A 2YH3_A 3PRW_A 3P1L_A 3Q7M_A 3Q7O_A 3Q7N_A ....
Probab=26.59 E-value=1.6e+02 Score=25.31 Aligned_cols=61 Identities=18% Similarity=0.267 Sum_probs=38.9
Q ss_pred ccCChhhhcceEEEEecCeEEEcccC-ceeec--cCCCeEEEEEcCCCceeeecCCCCcccccc
Q 019559 256 KYLGPKEREEFEVVVESGKLVYRQTG-MFVNT--NEDSKWIFVLSTSRALYVGQKKKGVFQHSS 316 (339)
Q Consensus 256 ~YL~p~ERe~YeV~VedGkL~yk~sg-~~vdT--~~~~kWIFVmdts~~LYvG~KkkG~FQHSS 316 (339)
-|..-.+..-|.+...+|+++|..+- ..+.. .-.+.-|||...++.||+=..+.|..-.+.
T Consensus 39 v~~~~~~~~l~~~d~~tG~~~W~~~~~~~~~~~~~~~~~~v~v~~~~~~l~~~d~~tG~~~W~~ 102 (238)
T PF13360_consen 39 VYVASGDGNLYALDAKTGKVLWRFDLPGPISGAPVVDGGRVYVGTSDGSLYALDAKTGKVLWSI 102 (238)
T ss_dssp EEEEETTSEEEEEETTTSEEEEEEECSSCGGSGEEEETTEEEEEETTSEEEEEETTTSCEEEEE
T ss_pred EEEEcCCCEEEEEECCCCCEEEEeeccccccceeeecccccccccceeeeEecccCCcceeeee
Confidence 34443444445555558999888862 22111 112455888888889999888888887774
No 15
>cd05727 Ig2_Contactin-2-like Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins. Ig2_Contactin-2-like: second Ig domain of the neural cell adhesion molecule contactin-2. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-2 (aliases TAG-1, axonin-1) facilitates cell adhesion by homophilic binding between molecules in apposed membranes. The first four Ig domains form the intermolecular binding fragment which arranges as a compact U-shaped module by contacts between Ig domains 1 and 4, and domains 2 and 3. It has been proposed that a linear zipper-like array forms, from contactin-2 molecules alternatively provided by the two apposed membranes.
Probab=25.89 E-value=1.4e+02 Score=24.71 Aligned_cols=34 Identities=21% Similarity=0.256 Sum_probs=23.8
Q ss_pred eEEEcccCceeeccCCCeEEEEEcCCCceeeecCC
Q 019559 274 KLVYRQTGMFVNTNEDSKWIFVLSTSRALYVGQKK 308 (339)
Q Consensus 274 kL~yk~sg~~vdT~~~~kWIFVmdts~~LYvG~Kk 308 (339)
.+.|-+++.+.....+... ||...+|+||+..-.
T Consensus 35 ~~~W~k~~~~~~~~~d~r~-~~~~~~G~L~fs~v~ 68 (96)
T cd05727 35 SYRWLLNEFPNFIPEDGRR-FVSQTNGNLYIAKVE 68 (96)
T ss_pred EEEEEECCcccccccCCCe-EEeCCCCcEEEeecC
Confidence 4568888887654444443 677778999998763
No 16
>TIGR03300 assembly_YfgL outer membrane assembly lipoprotein YfgL. Members of this protein family are YfgL, a lipoprotein component of a complex that acts protein insertion into the bacterial outer membrane. Other members of this complex are NlpB, YfiO, and YaeT. This protein contains multiple copies of a repeat that, in other contexts, are associated with binding of the coenzyme PQQ.
Probab=25.00 E-value=1.9e+02 Score=27.50 Aligned_cols=48 Identities=17% Similarity=0.202 Sum_probs=23.1
Q ss_pred ceEEEEecCeEEEccc-Cceeecc--CCCeEEEEEcCCCceeeecCCCCcc
Q 019559 265 EFEVVVESGKLVYRQT-GMFVNTN--EDSKWIFVLSTSRALYVGQKKKGVF 312 (339)
Q Consensus 265 ~YeV~VedGkL~yk~s-g~~vdT~--~~~kWIFVmdts~~LYvG~KkkG~F 312 (339)
-|.+...+|+++|..+ +..+... -++..+||.+.++.||+=....|..
T Consensus 77 v~a~d~~tG~~~W~~~~~~~~~~~p~v~~~~v~v~~~~g~l~ald~~tG~~ 127 (377)
T TIGR03300 77 VVALDAETGKRLWRVDLDERLSGGVGADGGLVFVGTEKGEVIALDAEDGKE 127 (377)
T ss_pred EEEEEccCCcEeeeecCCCCcccceEEcCCEEEEEcCCCEEEEEECCCCcE
Confidence 3333344666666543 1111111 1245566666666666655544443
No 17
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=24.88 E-value=56 Score=24.49 Aligned_cols=34 Identities=47% Similarity=0.670 Sum_probs=20.3
Q ss_pred CCceEEeecCCCCccCCC--CCCcccccccccccCChhhhcceEEEE
Q 019559 226 QPFFYWLDVGDGKEVNLE--KCPRNVLQRQCIKYLGPKEREEFEVVV 270 (339)
Q Consensus 226 q~FFyWLD~G~Gk~v~le--~CpR~kL~~q~V~YL~p~ERe~YeV~V 270 (339)
.+|.|+||.|++++|-|+ +||. ..++-+.++|.|
T Consensus 13 ~~~g~fL~~~~~~~vlLp~~e~~~-----------~~~~Gd~v~VFv 48 (61)
T PF13509_consen 13 NEFGYFLDDGEGKEVLLPKSEVPE-----------PLKVGDEVEVFV 48 (61)
T ss_dssp -SSEEEEEETT-EEEEEEGGG-----------------TTSEEEEEE
T ss_pred eCCEEEEECCCCCEEEechHHcCC-----------CCCCCCEEEEEE
Confidence 468899999999998886 5553 145556666654
No 18
>TIGR02658 TTQ_MADH_Hv methylamine dehydrogenase heavy chain. This family consists of the heavy chain of methylamine dehydrogenase light chain, a periplasmic enzyme. The enzyme contains a tryptophan tryptophylquinone (TTQ) prothetic group derived from two Trp residues in the light subunity. The enzyme forms a complex with the type I blue copper protein amicyanin and a cytochrome. Electron transfer procedes from TQQ to the copper and then to the heme group of the cytochrome.
Probab=23.52 E-value=90 Score=31.44 Aligned_cols=70 Identities=10% Similarity=0.200 Sum_probs=42.0
Q ss_pred CCceEEeecCCCCc---cCCCCCCcccccccccccCChhhhcceEEEEecCeEEE---------cc-cCceeec------
Q 019559 226 QPFFYWLDVGDGKE---VNLEKCPRNVLQRQCIKYLGPKEREEFEVVVESGKLVY---------RQ-TGMFVNT------ 286 (339)
Q Consensus 226 q~FFyWLD~G~Gk~---v~le~CpR~kL~~q~V~YL~p~ERe~YeV~VedGkL~y---------k~-sg~~vdT------ 286 (339)
.+=.-=+|...+|- |+.+.|+. -|-+.+ ..+.++..||++.+ .. +-..++.
T Consensus 127 ~~~V~VvD~~~~kvv~ei~vp~~~~--------vy~t~e--~~~~~~~~Dg~~~~v~~d~~g~~~~~~~~vf~~~~~~v~ 196 (352)
T TIGR02658 127 SPAVGVVDLEGKAFVRMMDVPDCYH--------IFPTAN--DTFFMHCRDGSLAKVGYGTKGNPKIKPTEVFHPEDEYLI 196 (352)
T ss_pred CCEEEEEECCCCcEEEEEeCCCCcE--------EEEecC--CccEEEeecCceEEEEecCCCceEEeeeeeecCCccccc
Confidence 33344556666654 66778875 344333 33446667777665 22 2223332
Q ss_pred -c-----CCCeEEEEEcCCCceeeec
Q 019559 287 -N-----EDSKWIFVLSTSRALYVGQ 306 (339)
Q Consensus 287 -~-----~~~kWIFVmdts~~LYvG~ 306 (339)
. .+++|.||... |++|+=.
T Consensus 197 ~rP~~~~~dg~~~~vs~e-G~V~~id 221 (352)
T TIGR02658 197 NHPAYSNKSGRLVWPTYT-GKIFQID 221 (352)
T ss_pred cCCceEcCCCcEEEEecC-CeEEEEe
Confidence 2 27999999888 9999875
No 19
>PF00727 IL4: Interleukin 4 This family is a subset of the SCOP family; InterPro: IPR002354 Cytokines are protein messengers that carry information from cell to cell []. Interleukin is one such molecule, and participates in several B-cell activation processes: e.g., it enhances production and secretion of IgG1 and IgE []; it induces expression of class II major histocompatability complex (MHC) molecules on resting B-cells; and it regulates expression of the low affinity Fc receptor for IgE on lymphocytes and monocytes. Interleukin-4 (IL4) has a compact, globular fold (similar to other cytokines), stabilised by 3 disulphide bonds []. One half of the structure is dominated by a 4 alpha-helix bundle with a left-handed twist []. The helices are anti-parallel, with 2 overhand connections, which fall into a 2-stranded anti-parallel beta-sheet [].; GO: 0005136 interleukin-4 receptor binding, 0008083 growth factor activity, 0006955 immune response, 0005576 extracellular region; PDB: 1HIK_A 1HZI_A 1ITI_A 2INT_A 1RCB_A 1CYL_A 3QB7_A 1BBN_A 2B8Z_A 1ITM_A ....
Probab=21.40 E-value=94 Score=27.30 Aligned_cols=28 Identities=32% Similarity=0.464 Sum_probs=22.6
Q ss_pred CCccccCCCCCchHH---HHHHHHHHHhhhh
Q 019559 97 EPVVFHSPRPVSELD---AAATKLQKVYKSY 124 (339)
Q Consensus 97 ~~~~~~~p~~~~e~~---~AA~~IQKvYRgY 124 (339)
-|.+|..|+..+|.+ +||+.+|.+|..+
T Consensus 29 V~Dvfa~~KnttekEllCrAatvLr~~y~~h 59 (117)
T PF00727_consen 29 VADVFAAPKNTTEKELLCRAATVLRQFYSHH 59 (117)
T ss_dssp EE-GGGSSSSSSHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHhccCCCCCcchhhhHHHHHHHHHHhcc
Confidence 356888898888876 8999999999865
No 20
>COG4382 Mu-like prophage protein gp16 [Function unknown]
Probab=21.04 E-value=1.4e+02 Score=27.87 Aligned_cols=65 Identities=22% Similarity=0.057 Sum_probs=44.8
Q ss_pred HHHhhhcCCCCcccCCCCchhHHhHHHHHHHhHhhhcCCCChhHHHHHHHHHHHHHhcCCcccccchHHHHHHHhh
Q 019559 145 LDFAALKRSSVSFFNIEKPETALSRWARARTRAAKVGKGLSKDENAQKLALQHWLEAIDPRHRYGHNLHFYYDIWS 220 (339)
Q Consensus 145 ld~a~l~~~s~sff~~~k~etA~srW~Ra~~~A~kvGkGlskd~kAq~l~lqhwLE~iDprHRYG~NL~~Y~~~W~ 220 (339)
...|-++...---|..+.++||.++|.+-.+.++..+-|+..-.= ++. |++ ++|..|--|++.|.
T Consensus 75 kiRa~wkqm~k~Gf~~dp~~talns~~~~~~~e~~~~vg~~~wq~---------~~~-~a~-~f~kdlve~lkr~~ 139 (170)
T COG4382 75 KIRAGWKQMAKGGFHGDPHLTALNSAAMLDKVEALLTVGGKHWQY---------AHA-MAR-MFGKDLVEYLKRTQ 139 (170)
T ss_pred HHHhhhhhhccCCCCCChHHHHHHHHHHHHHHHHHhhhhhhhHHH---------HHh-hHH-HHHHHHHHHhhHHH
Confidence 345556677777888899999999999999999998887732211 121 334 56666666666664
No 21
>COG4632 EpsL Exopolysaccharide biosynthesis protein related to N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [Carbohydrate transport and metabolism]
Probab=20.74 E-value=1.4e+02 Score=30.23 Aligned_cols=63 Identities=21% Similarity=0.180 Sum_probs=41.1
Q ss_pred EEEEecCeEEEcccCceeeccCCCeEEEEEcCCCceeeecCCCCcccccccCCCCc-c-ccceeEEEecCe
Q 019559 267 EVVVESGKLVYRQTGMFVNTNEDSKWIFVLSTSRALYVGQKKKGVFQHSSFLSGGA-I-TAAGRLVAHDGI 335 (339)
Q Consensus 267 eV~VedGkL~yk~sg~~vdT~~~~kWIFVmdts~~LYvG~KkkG~FQHSSFLaGg~-t-~AAG~Lvv~dG~ 335 (339)
=++|.||+|+|.++=.-..- .+-.|+++.+|.|-||.-.+- -+=.+++|+ + .+-|-.-|+||.
T Consensus 156 GfqisdGklvkp~dw~~~t~---ae~~~aftkdG~lkVyg~~sp---a~ll~sngaeasf~fgp~LIkdgk 220 (320)
T COG4632 156 GFQISDGKLVKPYDWAGYTG---AEACVAFTKDGTLKVYGRESP---ADLLISNGAEASFAFGPWLIKDGK 220 (320)
T ss_pred EEEEeCCeEeecCChhhhcc---ccceEEEccCCcEEEcCCCCh---HHHHHhccceeeeeeccEEEecCC
Confidence 57788999999875443332 344888898999999853211 112333333 3 577888888885
Done!