Query 026378
Match_columns 239
No_of_seqs 137 out of 226
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:15:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026378.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026378hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3073 Protein required for 1 100.0 5.9E-61 1.3E-65 421.1 10.5 175 37-234 2-176 (236)
2 PF03587 EMG1: EMG1/NEP1 methy 100.0 7.6E-59 1.7E-63 403.3 9.1 143 91-234 1-143 (202)
3 PRK04171 ribosome biogenesis p 100.0 6E-55 1.3E-59 384.7 11.8 151 63-234 9-163 (222)
4 COG1756 Mra1 Uncharacterized c 100.0 2.9E-47 6.4E-52 335.7 11.4 142 91-234 19-164 (223)
5 PF01011 PQQ: PQQ enzyme repea 42.5 28 0.00062 22.2 2.5 17 155-171 3-19 (38)
6 PF03755 YicC_N: YicC-like fam 32.9 48 0.001 27.7 3.1 39 149-190 16-54 (159)
7 smart00314 RA Ras association 31.1 1.1E+02 0.0024 22.6 4.5 64 150-221 3-69 (90)
8 PF13570 PQQ_3: PQQ-like domai 29.5 62 0.0013 20.6 2.6 26 142-170 14-39 (40)
9 TIGR02500 type_III_yscD type I 25.4 2.4E+02 0.0052 27.1 6.8 57 133-191 276-332 (410)
10 PF02202 Tachykinin: Tachykini 24.1 11 0.00023 19.8 -1.4 8 177-184 4-11 (11)
11 PF02108 FliH: Flagellar assem 24.0 2E+02 0.0043 21.9 5.0 46 129-190 47-92 (128)
12 PF00788 RA: Ras association ( 23.6 76 0.0016 22.9 2.4 61 149-218 2-68 (93)
13 COG0302 FolE GTP cyclohydrolas 22.3 77 0.0017 28.7 2.6 76 134-232 18-118 (195)
14 PF04889 Cwf_Cwc_15: Cwf15/Cwc 22.3 43 0.00092 30.7 1.1 17 106-122 224-242 (244)
15 PF14714 KH_dom-like: KH-domai 20.2 76 0.0016 24.1 1.9 33 148-181 23-60 (80)
No 1
>KOG3073 consensus Protein required for 18S rRNA maturation and 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.9e-61 Score=421.07 Aligned_cols=175 Identities=58% Similarity=0.891 Sum_probs=161.4
Q ss_pred hhhccccccccccccccccCCcccccchhhhhhhhhcCCCCCCCCCCCCCCcEEEEecCCchheeecCCeeeeecchhhH
Q 026378 37 LNDSGKRAKLEKTSQNDNKKGEEDGQEEKDVVVHEMEGIPIAPSDQNTKRPGVIFVLEKASLEVAKVGKSYQILNSDDHS 116 (239)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~livVLe~A~Le~~k~gk~~~LLn~d~H~ 116 (239)
+.++...++.++++...+++|+| ..| .+.+++||||++|+||++|+| +|+|||||+|.
T Consensus 2 ~~e~~~~~~~~~~~~~k~d~~~~-----------------~l~----~~~~~~ivVL~~a~le~~Kvg-~y~ll~~d~h~ 59 (236)
T KOG3073|consen 2 AVESSRKAKKEKADRAKEDNDEE-----------------ALP----KTKKRLIVVLEGASLETAKVG-KYQLLNSDDHA 59 (236)
T ss_pred cchhhhhcccccccccccCcccc-----------------ccc----ccCCcEEEEecCCCchhhhhh-heeeeccchhh
Confidence 34556677778888887777775 112 568999999999999999999 89999999999
Q ss_pred HHHHhCCCCCCCCCCcHHHHHHHHhhcchhhhcCCccEEEEEecCCeEEEEcCCCCCCcchhHHHHHHHHHHHhCccccC
Q 026378 117 NFLRRNNKNPADYRPDIVHQALLSILDSRLTKAGRLQAVYVRTDKGVLFEVKPHVRLPRTYKRFAGIMLQLLQKLSITAV 196 (239)
Q Consensus 117 ~~m~kl~~~~~~~RPDIvHq~LL~LLDSPLNKaG~Lq~VYIhT~~g~lIeVsP~~RIPRty~RF~GLM~qLL~k~~I~~~ 196 (239)
++++|+++++.++||||+|||||+||||||||||+|| |||||..|+||||||++||||||+||+|||+||||+++|++.
T Consensus 60 ~~lkk~~rdp~d~rpDitHQ~Ll~LlDSPlNkAgkLq-Vyi~T~knvLiEvnp~~rIPrtfkrfsglMvqLLhKlsIra~ 138 (236)
T KOG3073|consen 60 NFLKKNNRDPADYRPDITHQCLLMLLDSPLNKAGKLQ-VYIHTAKNVLIEVNPQVRIPRTFKRFSGLMVQLLHKLSIRAV 138 (236)
T ss_pred HHHHhccCCHHhcCCcHHHHHHHHHhcCcccccceeE-EEEEccCceEEEecccccCCCCHHHHHHHHHHHHHHheEecc
Confidence 9999999999999999999999999999999999999 999999999999999999999999999999999999999999
Q ss_pred CCccceEEEEecccccccCCCCeEEEEeeccceeeccc
Q 026378 197 GKREKLLRVIKNPVTQYLPVNSRKIGCLLARQVSHIVQ 234 (239)
Q Consensus 197 ~~~e~LLkviknplt~~LP~~~~kIglS~~g~~v~~~~ 234 (239)
++.+.||+||||||++|||+||+||||||+|+++.-.+
T Consensus 139 d~~~kLlkVvKNPVtdHlPv~~~Ki~lSf~~p~l~~~~ 176 (236)
T KOG3073|consen 139 DGTEKLLKVVKNPVTDHLPVNSRKIGLSFSGPKLSNVR 176 (236)
T ss_pred CchHHHHHHhcCcccccCCCCccEEeecCCCcccccHH
Confidence 99999999999999999999999999999999876433
No 2
>PF03587 EMG1: EMG1/NEP1 methyltransferase; InterPro: IPR005304 Members of this family are essential for 40S ribosomal biogenesis. They play a role in the methylation reaction of pre-rRNA processing. The structure of EMG1 has revealed that it is a novel member of the superfamily of alpha/beta knot fold methyltransferases [, ].; GO: 0008168 methyltransferase activity; PDB: 3BBE_B 3BBD_B 3BBH_B 2V3K_A 3OII_B 3OIJ_B 3OIN_A 2V3J_A 3O7B_A.
Probab=100.00 E-value=7.6e-59 Score=403.27 Aligned_cols=143 Identities=49% Similarity=0.684 Sum_probs=127.0
Q ss_pred EEecCCchheeecCCeeeeecchhhHHHHHhCCCCCCCCCCcHHHHHHHHhhcchhhhcCCccEEEEEecCCeEEEEcCC
Q 026378 91 FVLEKASLEVAKVGKSYQILNSDDHSNFLRRNNKNPADYRPDIVHQALLSILDSRLTKAGRLQAVYVRTDKGVLFEVKPH 170 (239)
Q Consensus 91 vVLe~A~Le~~k~gk~~~LLn~d~H~~~m~kl~~~~~~~RPDIvHq~LL~LLDSPLNKaG~Lq~VYIhT~~g~lIeVsP~ 170 (239)
|||++|+||+++.+.+++|||+|+|+++|+++++++++|||||||||||+||||||||+|+|+ |||||.+|+||+|||.
T Consensus 1 ivL~~a~LE~v~~~~~~~LLd~~~H~~~m~k~~~~~k~~RPDIvH~~LL~lldSpLNk~G~L~-VYIhT~~~~lI~V~p~ 79 (202)
T PF03587_consen 1 IVLEEASLELVPRKPKYQLLDSSDHYNAMKKLPKDEKRGRPDIVHQCLLMLLDSPLNKAGKLQ-VYIHTIDNVLIEVSPQ 79 (202)
T ss_dssp EEEEEES--BEEGSCGCSB--HHHHCGGHTTTTTGGGCS-HHHHHHHHHHHHTSHHHHTT-EE-EEEEETTSEEEEE-TT
T ss_pred CCccCCeeeEecCCCCcCccchHHHHHHHHHcCCChhhcCcchHHHHHHHHhcChHHhCCcEE-EEEEecCCEEEEECCC
Confidence 799999999999999999999999999999999999999999999999999999999999999 9999999999999999
Q ss_pred CCCCcchhHHHHHHHHHHHhCccccCCCccceEEEEecccccccCCCCeEEEEeeccceeeccc
Q 026378 171 VRLPRTYKRFAGIMLQLLQKLSITAVGKREKLLRVIKNPVTQYLPVNSRKIGCLLARQVSHIVQ 234 (239)
Q Consensus 171 ~RIPRty~RF~GLM~qLL~k~~I~~~~~~e~LLkviknplt~~LP~~~~kIglS~~g~~v~~~~ 234 (239)
+||||||+||+|||+|||++|+|++++++++||+|++|||++|||.|+++||||.+|+.+++.+
T Consensus 80 ~RiPR~y~rF~gLm~qLL~~~~I~~~~~~~~Llkv~~~~l~~~l~~~~~~i~ls~~g~~~~~~~ 143 (202)
T PF03587_consen 80 TRIPRNYNRFVGLMEQLLKKGKIPAEESGEPLLKVIKNPLTDLLPPGSRKILLSEKGEKVDPKE 143 (202)
T ss_dssp ----SSHHHHHHHHHHHHHHSEEEETTSTCEEEEEECS-HHHHCCCTCEEEEEETTSCEE-HHH
T ss_pred CcCCcCHHHHHHHHHHHHhcCcccCCCCCCeeEEEEeCCHHHhcCCCCeEEEEcCCCCcCCHHH
Confidence 9999999999999999999999999988999999999999999999999999999999997653
No 3
>PRK04171 ribosome biogenesis protein; Provisional
Probab=100.00 E-value=6e-55 Score=384.68 Aligned_cols=151 Identities=30% Similarity=0.443 Sum_probs=134.7
Q ss_pred chhhhhhhhhcCCCCCCCCCCCCCCcEEEEecCCchheeecCC--eeeeecchhhHHHHHhCCCCCCCCCCcHHHHHHHH
Q 026378 63 EEKDVVVHEMEGIPIAPSDQNTKRPGVIFVLEKASLEVAKVGK--SYQILNSDDHSNFLRRNNKNPADYRPDIVHQALLS 140 (239)
Q Consensus 63 ~~~~~~~~~~~~~p~~~~~~~~~~~~livVLe~A~Le~~k~gk--~~~LLn~d~H~~~m~kl~~~~~~~RPDIvHq~LL~ 140 (239)
++++.+|.+|.+.|...++.. |+|| +++|||+++|+++|+++++++++|||||||||||+
T Consensus 9 s~LElvP~ei~~hp~v~~~a~------------------rr~K~p~~~LLd~~~H~~~m~kl~~~~~rgRPDIvHq~LL~ 70 (222)
T PRK04171 9 SALELVPREIWNHPAVVKNAR------------------RRGKKPEEMLLDSSLHYHAMKKLEDKEKRGRPDIVHISLLV 70 (222)
T ss_pred cccccCCHHHhcCcHHHhhHH------------------HcCCChhhhccChHHHHHHHHhCccchhccCCCHHHHHHHH
Confidence 455666666666665554321 2355 45699999999999999999999999999999999
Q ss_pred hhcchhhhcCCccEEEEEecCCeEEEEcCCCCCCcchhHHHHHHHHHHHhCccccCCCccceEEEEecccccccCCC--C
Q 026378 141 ILDSRLTKAGRLQAVYVRTDKGVLFEVKPHVRLPRTYKRFAGIMLQLLQKLSITAVGKREKLLRVIKNPVTQYLPVN--S 218 (239)
Q Consensus 141 LLDSPLNKaG~Lq~VYIhT~~g~lIeVsP~~RIPRty~RF~GLM~qLL~k~~I~~~~~~e~LLkviknplt~~LP~~--~ 218 (239)
+|||||||+|+|+ |||||.+|+||+|||++||||||+||+|||+|||++++|+++ +++||++++|||++|||.+ +
T Consensus 71 lldSpLNk~G~L~-VYIhT~~~~lI~V~P~~RiPR~y~rF~gLM~qLL~k~~I~~~--~~~Llkv~k~~l~~~l~~~~~~ 147 (222)
T PRK04171 71 ALDSPLNKEGKLR-VYIHTRDDKVIYVNPETRLPKNYNRFVGLMEQLLKEGRVPPN--GEPLLEIENKSLEELLEEIGPD 147 (222)
T ss_pred HhcChhhhcCCeE-EEEEecCCEEEEECCCCcCCCCHHHHHHHHHHHHHhCccCCC--CcchheeecCcHHHhccccCCC
Confidence 9999999999999 999999999999999999999999999999999999999986 7899999999999999999 9
Q ss_pred eEEEEeeccceeeccc
Q 026378 219 RKIGCLLARQVSHIVQ 234 (239)
Q Consensus 219 ~kIglS~~g~~v~~~~ 234 (239)
++||||.+|+.+++.+
T Consensus 148 ~~i~lS~~g~~~~~~~ 163 (222)
T PRK04171 148 RIILLSEKGELVKPKE 163 (222)
T ss_pred cEEEECCCCcccCHHH
Confidence 9999999999998653
No 4
>COG1756 Mra1 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.9e-47 Score=335.74 Aligned_cols=142 Identities=42% Similarity=0.569 Sum_probs=127.7
Q ss_pred EEecCCchheeecC-C--eeeeecchhhHHHHHhCCCCCCCCCCcHHHHHHHHhhcchhhhcCCccEEEEEecCCeEEEE
Q 026378 91 FVLEKASLEVAKVG-K--SYQILNSDDHSNFLRRNNKNPADYRPDIVHQALLSILDSRLTKAGRLQAVYVRTDKGVLFEV 167 (239)
Q Consensus 91 vVLe~A~Le~~k~g-k--~~~LLn~d~H~~~m~kl~~~~~~~RPDIvHq~LL~LLDSPLNKaG~Lq~VYIhT~~g~lIeV 167 (239)
|+...|+++.+|+. + ...|||+++||.+|+++...++||||||+|||||++||||||++|+|+ |||||++|.||+|
T Consensus 19 i~~hpav~~~akrrgk~p~~~iLd~~~hh~am~~l~~~e~RgRPDI~H~~LL~~lDSplnk~~~L~-vYIHT~~~~vI~v 97 (223)
T COG1756 19 IVNHPAVLRDAKRRGKRPEKIILDSSYHHTAMKKLEDRERRGRPDIVHQCLLTLLDSPLNKEGKLR-VYIHTRNDYVIEV 97 (223)
T ss_pred HhcCHHHHHHHHHhCCCCCcEEEecccCHHHHHHhcChhhcCCCchHHHHHHHHhhccccccccee-EEEEecCCEEEEE
Confidence 34445555565553 3 678999999999999998888999999999999999999999999999 9999999999999
Q ss_pred cCCCCCCcchhHHHHHHHHHHHhCccccCCCccceEEEEecccccccCCCC-eEEEEeeccceeeccc
Q 026378 168 KPHVRLPRTYKRFAGIMLQLLQKLSITAVGKREKLLRVIKNPVTQYLPVNS-RKIGCLLARQVSHIVQ 234 (239)
Q Consensus 168 sP~~RIPRty~RF~GLM~qLL~k~~I~~~~~~e~LLkviknplt~~LP~~~-~kIglS~~g~~v~~~~ 234 (239)
||.+|+||||+||+|||+|||++++|++++ +++||+++++||++|||.++ ..|-||..|....+++
T Consensus 98 ~p~~R~Prny~RFiGLmeqLlk~~~i~~~~-~e~Ll~v~~~~l~d~l~~~~~~~ill~e~G~~~~p~~ 164 (223)
T COG1756 98 NPETRLPRNYNRFIGLMEQLLKKGRIPSNG-GETLLEVEKNPLTDLLPENNKVTILLHEKGELIPPKE 164 (223)
T ss_pred CCCccCCCCHHHHHHHHHHHHhcCCcCCCC-CcEeeeeecCcHHHhccccCceEEEEcCCCCccCHHH
Confidence 999999999999999999999999999874 89999999999999999998 6688999988877653
No 5
>PF01011 PQQ: PQQ enzyme repeat family.; InterPro: IPR002372 Pyrrolo-quinoline quinone (PQQ) is a redox coenzyme, which serves as a cofactor for a number of enzymes (quinoproteins) and particularly for some bacterial dehydrogenases [, ]. A number of bacterial quinoproteins belong to this family. Enzymes in this group have repeats of a beta propeller.; PDB: 1H4I_C 1H4J_E 1W6S_A 2YH3_A 3PRW_A 3P1L_A 3Q7M_A 3Q7O_A 3Q7N_A 1G72_A ....
Probab=42.50 E-value=28 Score=22.24 Aligned_cols=17 Identities=35% Similarity=0.661 Sum_probs=15.0
Q ss_pred EEEEecCCeEEEEcCCC
Q 026378 155 VYVRTDKGVLFEVKPHV 171 (239)
Q Consensus 155 VYIhT~~g~lIeVsP~~ 171 (239)
||++|.+|.|+.++..+
T Consensus 3 v~~~~~~g~l~AlD~~T 19 (38)
T PF01011_consen 3 VYVGTPDGYLYALDAKT 19 (38)
T ss_dssp EEEETTTSEEEEEETTT
T ss_pred EEEeCCCCEEEEEECCC
Confidence 99999999999998653
No 6
>PF03755 YicC_N: YicC-like family, N-terminal region ; InterPro: IPR013527 Proteins in this entry are homologues of YicC (P23839 from SWISSPROT) from Escherichia coli. Although it is relatively poorly characterised YicC has been shown to be important for cells in the stationary phase, and essential for growth at high temperatures []. This domain is found at the N-terminal region of these proteins.
Probab=32.89 E-value=48 Score=27.72 Aligned_cols=39 Identities=21% Similarity=0.490 Sum_probs=31.6
Q ss_pred cCCccEEEEEecCCeEEEEcCCCCCCcchhHHHHHHHHHHHh
Q 026378 149 AGRLQAVYVRTDKGVLFEVKPHVRLPRTYKRFAGIMLQLLQK 190 (239)
Q Consensus 149 aG~Lq~VYIhT~~g~lIeVsP~~RIPRty~RF~GLM~qLL~k 190 (239)
.+.+. |=|++.+++-.+|+ +|+|+.|.-|..-+-+++.+
T Consensus 16 ~~~~~-vEikSvN~R~Ldi~--~rlP~~l~~lE~~ir~~i~~ 54 (159)
T PF03755_consen 16 GGSIS-VEIKSVNHRFLDIS--IRLPRELSSLEPEIRKLIRK 54 (159)
T ss_pred CeEEE-EEEEecccCceeeE--EeCCHHHHHHHHHHHHHHHH
Confidence 46778 99999999988885 89999999887766666555
No 7
>smart00314 RA Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.)
Probab=31.10 E-value=1.1e+02 Score=22.58 Aligned_cols=64 Identities=22% Similarity=0.284 Sum_probs=45.2
Q ss_pred CCccEEEEEe---cCCeEEEEcCCCCCCcchhHHHHHHHHHHHhCccccCCCccceEEEEecccccccCCCCeEE
Q 026378 150 GRLQAVYVRT---DKGVLFEVKPHVRLPRTYKRFAGIMLQLLQKLSITAVGKREKLLRVIKNPVTQYLPVNSRKI 221 (239)
Q Consensus 150 G~Lq~VYIhT---~~g~lIeVsP~~RIPRty~RF~GLM~qLL~k~~I~~~~~~e~LLkviknplt~~LP~~~~kI 221 (239)
+-|+ ||... ..-+.|.|++.+... .++.++|++..+..+-..=.|..++.+.....|+++...+
T Consensus 3 ~~lr-V~~~~~~~~~~kti~v~~~tTa~-------~Vi~~~l~k~~l~~~~~~y~L~e~~~~~~er~L~~~e~Pl 69 (90)
T smart00314 3 FVLR-VYVDDLPGGTYKTLRVSSRTTAR-------DVIQQLLEKFHLTDDPEEYVLVEVLPDGKERVLPDDENPL 69 (90)
T ss_pred eEEE-EecccCCCCcEEEEEECCCCCHH-------HHHHHHHHHhCCCCCcccEEEEEEeCCcEEEEeCCCCcce
Confidence 5577 88766 445688888887654 7899999999997642345677777566667776665554
No 8
>PF13570 PQQ_3: PQQ-like domain; PDB: 3HXJ_B 3Q54_A.
Probab=29.46 E-value=62 Score=20.56 Aligned_cols=26 Identities=31% Similarity=0.515 Sum_probs=17.9
Q ss_pred hcchhhhcCCccEEEEEecCCeEEEEcCC
Q 026378 142 LDSRLTKAGRLQAVYVRTDKGVLFEVKPH 170 (239)
Q Consensus 142 LDSPLNKaG~Lq~VYIhT~~g~lIeVsP~ 170 (239)
..||.--.| . |||-|.+|.|+.+++.
T Consensus 14 ~~~~~v~~g--~-vyv~~~dg~l~ald~~ 39 (40)
T PF13570_consen 14 WSSPAVAGG--R-VYVGTGDGNLYALDAA 39 (40)
T ss_dssp -S--EECTS--E-EEEE-TTSEEEEEETT
T ss_pred CcCCEEECC--E-EEEEcCCCEEEEEeCC
Confidence 356665555 4 9999999999999975
No 9
>TIGR02500 type_III_yscD type III secretion apparatus protein, YscD/HrpQ family. This family represents a conserved protein of bacterial type III secretion systems. Gene symbols are variable from species to species. Members are designated YscD in Yersinia, HrpQ in Pseudomonas syringae, and EscD in enteropathogenic Escherichia coli. In the Chlamydiae, this model describes the C-terminal 400 residues of a longer protein.
Probab=25.37 E-value=2.4e+02 Score=27.13 Aligned_cols=57 Identities=21% Similarity=0.271 Sum_probs=49.5
Q ss_pred HHHHHHHHhhcchhhhcCCccEEEEEecCCeEEEEcCCCCCCcchhHHHHHHHHHHHhC
Q 026378 133 IVHQALLSILDSRLTKAGRLQAVYVRTDKGVLFEVKPHVRLPRTYKRFAGIMLQLLQKL 191 (239)
Q Consensus 133 IvHq~LL~LLDSPLNKaG~Lq~VYIhT~~g~lIeVsP~~RIPRty~RF~GLM~qLL~k~ 191 (239)
.+|-.++.-|++-|-+.|+++ +.+-+..+.-|.++-.+.-... .+|..+..+|-+..
T Consensus 276 ~~~~~~~~~L~~~L~~~gL~~-~~~~~~~~~~i~lsG~l~~~~~-~~~~~~l~~f~~~~ 332 (410)
T TIGR02500 276 RVASDVIAQLASLLSDAGLLG-VVTVTESGREIALSGQLDSEKR-SRLQELLAAFKQRD 332 (410)
T ss_pred echHHHHHHHHHHHHHCCCCc-eEEEEecCCEEEEEecCCHHHH-HHHHHHHHHHHHhC
Confidence 467777789999999999999 9999999999999999986655 99999998888873
No 10
>PF02202 Tachykinin: Tachykinin family; InterPro: IPR002040 This family includes peptides, which belong to the tachykinin family. Tachykinins [, , ] are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. Tachykinins, like most other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. Tachykinins are from ten to twelve residues long.; GO: 0007217 tachykinin receptor signaling pathway, 0007268 synaptic transmission; PDB: 1MYU_A 1N6T_A 2GFR_A.
Probab=24.13 E-value=11 Score=19.80 Aligned_cols=8 Identities=38% Similarity=0.725 Sum_probs=5.3
Q ss_pred hhHHHHHH
Q 026378 177 YKRFAGIM 184 (239)
Q Consensus 177 y~RF~GLM 184 (239)
-++|.|||
T Consensus 4 pd~F~GLM 11 (11)
T PF02202_consen 4 PDQFYGLM 11 (11)
T ss_dssp HHHHCCC-
T ss_pred cccceecC
Confidence 46788887
No 11
>PF02108 FliH: Flagellar assembly protein FliH; InterPro: IPR018035 This entry represents a region found in the flagellar assembly protein FliH, as well as in type III secretion system protein HrpE. Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export []. The sequence of fliH has been deduced and shown to encode a protein of molecular mass of 25,782 Da. Bacterial HrpE proteins are belived to function on the type III secretion system, specifically the secretion of HrpZ (harpinPss) [].
Probab=24.04 E-value=2e+02 Score=21.91 Aligned_cols=46 Identities=13% Similarity=0.291 Sum_probs=31.3
Q ss_pred CCCcHHHHHHHHhhcchhhhcCCccEEEEEecCCeEEEEcCCCCCCcchhHHHHHHHHHHHh
Q 026378 129 YRPDIVHQALLSILDSRLTKAGRLQAVYVRTDKGVLFEVKPHVRLPRTYKRFAGIMLQLLQK 190 (239)
Q Consensus 129 ~RPDIvHq~LL~LLDSPLNKaG~Lq~VYIhT~~g~lIeVsP~~RIPRty~RF~GLM~qLL~k 190 (239)
.+|+++-..+-.++++.+...+.+. ||+| |.+|........+.+..
T Consensus 47 ~~~~~i~~~i~~al~~~~~~~~~v~-I~v~---------------p~d~~~l~~~~~~~~~~ 92 (128)
T PF02108_consen 47 EDPEAILNLIREALQELPRDEEKVT-IRVH---------------PDDYEALEELLEDELPE 92 (128)
T ss_pred cCHHHHHHHHHHHHHHhhccCCCeE-EEEC---------------HHHHHHHHHHHHHHHhh
Confidence 4577776667777766667778888 8887 66777766665544443
No 12
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=23.57 E-value=76 Score=22.86 Aligned_cols=61 Identities=16% Similarity=0.133 Sum_probs=40.0
Q ss_pred cCCccEEEEEecC----CeEEEEcCCCCCCcchhHHHHHHHHHHHhCccccCCCccceE--EEEecccccccCCCC
Q 026378 149 AGRLQAVYVRTDK----GVLFEVKPHVRLPRTYKRFAGIMLQLLQKLSITAVGKREKLL--RVIKNPVTQYLPVNS 218 (239)
Q Consensus 149 aG~Lq~VYIhT~~----g~lIeVsP~~RIPRty~RF~GLM~qLL~k~~I~~~~~~e~LL--kviknplt~~LP~~~ 218 (239)
.|-|+ ||..... -+.|.|++.+.. ..++.++|++..+ +.+....-| -.........|+++.
T Consensus 2 ~~~lr-Vy~~~~~~~~~~k~i~v~~~tTa-------~evi~~~l~k~~l-~~~~~~y~L~~~~~~~~~er~L~~~E 68 (93)
T PF00788_consen 2 SGVLR-VYDGDGSPGSTYKTIKVSSSTTA-------REVIEMALEKFGL-AEDPSDYCLVEVEESGGEERPLDDDE 68 (93)
T ss_dssp EEEEE-EEETTSSSCCSEEEEEEETTSBH-------HHHHHHHHHHTTT-SSSGGGEEEEEEECTTTEEEEETTTS
T ss_pred CeEEE-EEcCCCCCCccEEEEEECCCCCH-------HHHHHHHHHHhCC-CCCCCCEEEEEEEcCCCEEEEcCCCC
Confidence 35678 8888776 678889888765 4899999999999 333344444 333344444444443
No 13
>COG0302 FolE GTP cyclohydrolase I [Coenzyme metabolism]
Probab=22.35 E-value=77 Score=28.66 Aligned_cols=76 Identities=21% Similarity=0.301 Sum_probs=49.0
Q ss_pred HHHHHHHhhcchhhhcCCccEEEEEecCCeEEEEcCCCCCCcchhHHHHHHHHHHHhCccccC---------CCccceEE
Q 026378 134 VHQALLSILDSRLTKAGRLQAVYVRTDKGVLFEVKPHVRLPRTYKRFAGIMLQLLQKLSITAV---------GKREKLLR 204 (239)
Q Consensus 134 vHq~LL~LLDSPLNKaG~Lq~VYIhT~~g~lIeVsP~~RIPRty~RF~GLM~qLL~k~~I~~~---------~~~e~LLk 204 (239)
.-..||.++---.|++|.+. |.+|+..+|..|+.-....+. ++.+-+.-
T Consensus 18 avr~lL~~~Gedp~reGL~~----------------------TP~RVak~~~e~f~G~~~~~~~~~l~~~fe~~~~emVl 75 (195)
T COG0302 18 AVRELLEALGEDPDREGLLE----------------------TPKRVAKAYRELFSGYDEDPAEIVLEATFEEDHDEMVL 75 (195)
T ss_pred HHHHHHHHhCCCCCchhhhh----------------------hHHHHHHHHHHHHhhhCCChHHhhhcccccccCccEEE
Confidence 34567888888889999888 899999999888876555433 11111222
Q ss_pred EEecccc----------------cccCCCCeEEEEeeccceeec
Q 026378 205 VIKNPVT----------------QYLPVNSRKIGCLLARQVSHI 232 (239)
Q Consensus 205 viknplt----------------~~LP~~~~kIglS~~g~~v~~ 232 (239)
|-.-++. -|+| |.+.+|||-=+++|.+
T Consensus 76 vkdI~f~S~CEHHllPf~GkahVAYiP-~gkV~GlSKiaRiV~~ 118 (195)
T COG0302 76 VKDIEFYSLCEHHLLPFFGKAHVAYIP-DGKVIGLSKIARIVDI 118 (195)
T ss_pred EeccceeeecccccccccceEEEEEcC-CCceecHHHHHHHHHH
Confidence 2222222 2567 7778899977666643
No 14
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=22.35 E-value=43 Score=30.66 Aligned_cols=17 Identities=35% Similarity=0.569 Sum_probs=14.4
Q ss_pred eee--eecchhhHHHHHhC
Q 026378 106 SYQ--ILNSDDHSNFLRRN 122 (239)
Q Consensus 106 ~~~--LLn~d~H~~~m~kl 122 (239)
.|+ +|.++.|..||.|.
T Consensus 224 ~fiND~~rSdfH~kFl~Ky 242 (244)
T PF04889_consen 224 EFINDTLRSDFHKKFLNKY 242 (244)
T ss_pred CcccCCcccHHHHHHHHHh
Confidence 465 99999999999874
No 15
>PF14714 KH_dom-like: KH-domain-like of EngA bacterial GTPase enzymes, C-terminal; PDB: 2HJG_A 1MKY_A.
Probab=20.19 E-value=76 Score=24.10 Aligned_cols=33 Identities=36% Similarity=0.623 Sum_probs=22.3
Q ss_pred hcCCccEEEEEecCCe-----EEEEcCCCCCCcchhHHH
Q 026378 148 KAGRLQAVYVRTDKGV-----LFEVKPHVRLPRTYKRFA 181 (239)
Q Consensus 148 KaG~Lq~VYIhT~~g~-----lIeVsP~~RIPRty~RF~ 181 (239)
+.++++ ||--|.-+. +|.+|-.-.+|.+|.||.
T Consensus 23 ~g~~~K-i~Y~tQv~~~PPtFv~f~N~~~~~~~sY~ryL 60 (80)
T PF14714_consen 23 KGKRLK-IYYATQVGTRPPTFVLFVNDPELLPESYKRYL 60 (80)
T ss_dssp TTCC---EEEEEEEETTTTEEEEEES-CCC--HHHHHHH
T ss_pred CCceeE-EEEEEeCCCCCCEEEEEeCCcccCCHHHHHHH
Confidence 567888 766665554 999999999999999996
Done!