RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013738
(437 letters)
>gnl|CDD|211336 cd02569, PseudoU_synth_ScPus3, Pseudouridine synthase,
Saccharomyces cerevisiae Pus3 like. This group consists
of eukaryotic pseudouridine synthases similar to S.
cerevisiae Pus3p, mouse Pus3p and, human PUS2.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required. S.
cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse
Pus3p has been shown to makes psi38 and, possibly also
psi 39, in tRNAs. Psi38 and psi39 are highly conserved
in tRNAs from eubacteria, archea and eukarya.
Length = 256
Score = 390 bits (1003), Expect = e-136
Identities = 141/259 (54%), Positives = 179/259 (69%), Gaps = 4/259 (1%)
Query: 96 LKVMYFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKGVSSVG 155
L+ Y G + GFA TVE +F+ALEKTRL + D++ S+YSRCGRTDKGVS+ G
Sbjct: 1 LRFAYLGWNYNGFAVQEETTNTVEETLFEALEKTRL-IEDRQTSNYSRCGRTDKGVSAFG 59
Query: 156 QVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSPAPTDF 215
QVI++ +RSN+K + + S V+ E+E+ Y ++LNRVLP DIR++ W+P P DF
Sbjct: 60 QVISLDVRSNLKPEDGLDPSTD--VKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDF 117
Query: 216 SARFSCISREYKYFFWRENLNLSAMESAGKKFVGEHDFRNFCKMDAAN-VHNYKRHVTSF 274
SARFSC+SR Y+YFF + +L++ M A K +GEHDFRNFCKMD AN V NY R V S
Sbjct: 118 SARFSCVSRTYRYFFPKGDLDIELMRKAAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSA 177
Query: 275 EISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIGQGLESIDVIESLLDTNGIPR 334
E+ P +G+ L ++RGSAFLWHQVRCM+AVLF+IGQGLE VI LLD PR
Sbjct: 178 EVEPVDQHPDGDGLYYFEVRGSAFLWHQVRCMMAVLFLIGQGLEPPSVISQLLDVEKNPR 237
Query: 335 KPQYNMAPEIPLVLQSCDF 353
KPQY MA E+PLVL C F
Sbjct: 238 KPQYTMASEVPLVLYDCGF 256
>gnl|CDD|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal
structure and biogenesis].
Length = 266
Score = 217 bits (554), Expect = 5e-68
Identities = 87/291 (29%), Positives = 122/291 (41%), Gaps = 52/291 (17%)
Query: 91 KRYVALKVMYFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKG 150
KR ALK+ Y G RF+G+ N+ TV+ E+ KAL K + GRTD G
Sbjct: 2 KRI-ALKIAYDGTRFHGWQRQPNV-RTVQGELEKALSK-----IGGESVRVIGAGRTDAG 54
Query: 151 VSSVGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSP 210
V ++GQV+ ++ VR LN +LP DIRV+ +
Sbjct: 55 VHALGQVVHFDTPADRPL--------------------EKLVRALNALLPPDIRVLDVAE 94
Query: 211 APTDFSARFSCISREYKYFFWREN----------------LNLSAMESAGKKFVGEHDFR 254
P DF ARFS SR Y+Y + L+L AM A K +G HDF
Sbjct: 95 VPDDFHARFSAKSRTYRYIIYNAPLRPPFLANYVWHVPYPLDLDAMREAAKLLLGTHDFT 154
Query: 255 NFCKMDAANVHNYKRHVTSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIG 314
+F K + R + ++S L I I G++FLWH VR +V L ++G
Sbjct: 155 SFRKAG-CQSKSPVRTIYRIDVS------RDGDLIVIDISGNSFLWHMVRNIVGALLLVG 207
Query: 315 QGLESIDVIESLLDTNGIPRKPQYNMAPEIPLVLQSCDFDGLKFTCSLDAG 365
+G ++ I+ LL+ RK AP L L D+ G
Sbjct: 208 RGKRPVEWIKELLE--AKDRKLAGPTAPAEGLYLVRVDYPEDFELPEDALG 256
>gnl|CDD|232810 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase. Members
of this family are the tRNA modification enzyme TruA,
tRNA pseudouridine(38-40) synthase. In a few species
(e.g. Bacillus anthracis), TruA is represented by two
paralogs [Protein synthesis, tRNA and rRNA base
modification].
Length = 227
Score = 186 bits (475), Expect = 9e-57
Identities = 78/253 (30%), Positives = 115/253 (45%), Gaps = 41/253 (16%)
Query: 92 RYVALKVMYFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKGV 151
R +ALK+ Y G ++G+ N TV+ E+ KALE + K GRTDKGV
Sbjct: 1 RKIALKIAYDGSNYHGWQRQPNK-RTVQGELEKALEA---IGKKKITIM--SAGRTDKGV 54
Query: 152 SSVGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSPA 211
++GQVI+ I + N LN +LP DIRV +P
Sbjct: 55 HAMGQVISFDTPKEIPDNKLN--------------------AKLNALLPPDIRVKALAPV 94
Query: 212 PTDFSARFSCISREYKYFF-----WRENLNLSAMESAGKKFVGEHDFRNFCKMDAANVHN 266
+F ARFS R Y+Y + L+L M +A K+ +G+HDF NF K + +
Sbjct: 95 NDNFHARFSASKRHYRYILYNHRHYYSPLDLEKMRAAAKQLLGKHDFSNFSKAKSK-SRS 153
Query: 267 YKRHVTSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIGQGLESIDVIESL 326
R ++ ++S E + I G++FLWH VR +V L ++G+G + + L
Sbjct: 154 PIRTISDIKVS------ESGEYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKL 207
Query: 327 LD---TNGIPRKP 336
LD N P
Sbjct: 208 LDAKKRNLAPTTA 220
>gnl|CDD|211322 cd00497, PseudoU_synth_TruA_like, Pseudouridine synthase, TruA
family. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases similar to
Escherichia coli TruA, Saccharomyces cerevisiae Pus1p,
S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and
human PUS1. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. S. cerevisiae PUS1 catalyzes the formation of
psi34 and psi36 in the intron containing tRNAIle, psi35
in the intron containing tRNATyr, psi27 and/or psi28 in
several yeast cytoplasmic tRNAs and, psi44 in U2 small
nuclear RNA (U2 snRNA). The presence of the intron is
required for the formation of psi 34, 35 and 36. In
addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C.
elegans Pus1p does not modify psi44 in U2 snRNA. S.
cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44
in U2 snRNA and, psi38 and psi39 in tRNAs are highly
phylogenetically conserved. Psi 26,27,28,34,35,36,65
and 67 in tRNAs are less highly conserved. Mouse Pus1p
regulates nuclear receptor activity through
pseudouridylation of Steroid Receptor RNA Activator.
Missense mutation in human PUS1 causes mitochondrial
myopathy and sideroblastic anemia (MLASA).
Length = 215
Score = 181 bits (461), Expect = 6e-55
Identities = 77/254 (30%), Positives = 106/254 (41%), Gaps = 41/254 (16%)
Query: 100 YFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKGVSSVGQVIA 159
Y G +++GF N PTVE E+ AL + RTD+GVS++GQV+A
Sbjct: 3 YDGTKYHGFQR-QNDVPTVEGELIIALL--KAGNIPYF---IKAAARTDRGVSALGQVVA 56
Query: 160 IYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSPAPTDFSARF 219
I LN +LP DIRV P DF A
Sbjct: 57 IETERR------------------------LTPEALNGILPGDIRVFAVHSVPPDFHAPR 92
Query: 220 SCISREYKYFFWRENLNLSAMESAGKKFVGEHDFRNFCKMDAANVHNYKRHVTSFEISPC 279
C R Y+Y+ L+ ++SA +F+G HDF NF K D N R + S E
Sbjct: 93 YCDHRTYRYYIPSFPLDDERLKSAASRFLGTHDFTNFSKKDT---RNTVRTIISIECK-- 147
Query: 280 YISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIGQGLESIDVIESLLDTNGIPRKPQYN 339
+ N ++ + +FLWHQVR MV L ++G+GL S + LL G
Sbjct: 148 ----DLNPFVVVEFKAKSFLWHQVRRMVGFLMLVGEGLHSPSSVSRLLA--GPAPPIPMV 201
Query: 340 MAPEIPLVLQSCDF 353
AP L+L +
Sbjct: 202 PAPAEGLLLVDVKY 215
>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated.
Length = 244
Score = 171 bits (435), Expect = 1e-50
Identities = 67/254 (26%), Positives = 102/254 (40%), Gaps = 50/254 (19%)
Query: 91 KRYVALKVMYFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKG 150
R AL + Y G F+G+ N TV+ E+ KAL K + GRTD G
Sbjct: 2 MRI-ALTIEYDGTNFHGWQRQPN-GRTVQGELEKALSKL-----AGEPVRVIGAGRTDAG 54
Query: 151 VSSVGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSP 210
V ++GQV + + R LN +LP DI V+
Sbjct: 55 VHALGQVAHFDTPAPR--------------------PPEKWRRALNALLPDDIAVLWAEE 94
Query: 211 APTDFSARFSCISREYKYFFWREN----------------LNLSAMESAGKKFVGEHDFR 254
P DF ARFS +R Y+Y + L++ AM A + +GEHDF
Sbjct: 95 VPDDFHARFSAKARRYRYRIYNRPARPPFLRGYVWHYPYPLDVDAMNEAAQYLLGEHDFT 154
Query: 255 NFCKMDAANVHNYKRHVTSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIG 314
+F + R + + ++ EG+ + I + FL + VR +V L +G
Sbjct: 155 SFRA-SGCQSKSPVRTIYEAD-----VTREGDFIV-FDISANGFLHNMVRNIVGTLLEVG 207
Query: 315 QGLESIDVIESLLD 328
+G + I+ LL+
Sbjct: 208 KGKRPPEDIKELLE 221
>gnl|CDD|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional.
Length = 265
Score = 163 bits (413), Expect = 3e-47
Identities = 85/268 (31%), Positives = 121/268 (45%), Gaps = 44/268 (16%)
Query: 95 ALKVMYFGQRFYGFASDGNMEP---TVESEIFKALEKTRLLVADKKESHYSRCGRTDKGV 151
A ++ Y G RF+G +P TVE E A + L +D +E+ ++ GRTD+GV
Sbjct: 4 AFRISYIGTRFFG----SQYQPDQRTVEGEFIAACRRLGLF-SDWREAGFALAGRTDRGV 58
Query: 152 SSVGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSPA 211
+ GQV+A +T+ V LN LP DI GW+
Sbjct: 59 HARGQVLAF---------STHKPERA--------------VEALNGQLPPDIWCTGWAEV 95
Query: 212 PTDFSARFSCISREYKYFFWRENLNLSAMESAGKKFVGEHDFRNFCKMDAANVHNYKRHV 271
P F R+ ISR Y+Y+F R +++AM A +F+G HDF F +++ + R +
Sbjct: 96 PESFHPRYDAISRTYRYYFSRPPSDINAMRDAAGEFIGTHDFSCFARVEGKSP---VRTI 152
Query: 272 TSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIGQGLESIDVIESLLDTNG 331
+ F ++ +FLWH VRCM L IG+G D IE LL +
Sbjct: 153 LRIRV------FSDGGFPVFEVTAQSFLWHMVRCMAGALLQIGEGEMEPDDIERLL-SGP 205
Query: 332 IPRKPQYNMAPEIPLVLQSCDFDGLKFT 359
RK + AP LVL D GL FT
Sbjct: 206 CKRKVK--PAPAEGLVLWDVDC-GLTFT 230
>gnl|CDD|211337 cd02570, PseudoU_synth_EcTruA, Eukaryotic and bacterial
pseudouridine synthases similar to E. coli TruA. This
group consists of eukaryotic and bacterial pseudouridine
synthases similar to E. coli TruA, Pseudomonas
aeruginosa truA and human pseudouridine synthase-like 1
(PUSL1). Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. E. coli TruA makes psi38/39 and/or 40 in tRNA.
psi38 and psi39 in tRNAs are highly phylogenetically
conserved. P. aeruginosa truA is required for induction
of type III secretory genes and may act through
modifying tRNAs critical for the expression of type III
genes or their regulators.
Length = 239
Score = 154 bits (391), Expect = 3e-44
Identities = 72/254 (28%), Positives = 106/254 (41%), Gaps = 59/254 (23%)
Query: 96 LKVMYFGQRFYGFASDGNMEPTVESEIFKAL-----EKTRLLVADKKESHYSRCGRTDKG 150
L + Y G F G+ N TV+ E+ KAL E R++ A GRTD G
Sbjct: 1 LTIEYDGTNFSGWQRQPN-GRTVQGELEKALSKIAGEPVRVIGA----------GRTDAG 49
Query: 151 VSSVGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSP 210
V ++GQV S I ++ LN +LP DIRV+
Sbjct: 50 VHALGQVAHFDTPSEI--------------------PLEKLIKALNSLLPPDIRVLSAEE 89
Query: 211 APTDFSARFSCISREYKYF----------------FWRENLNLSAMESAGKKFVGEHDFR 254
P DF ARFS SR Y+Y L++ AM+ A K +G HDF
Sbjct: 90 VPDDFHARFSAKSRTYRYRILNRPVPSPFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFS 149
Query: 255 NFCKMDAANVHNYKRHVTSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIG 314
+F + R + ++ EG+ + +IR + FL+H VR +V L +G
Sbjct: 150 SFRAAG-CQSKSTVRTIYRADVYR-----EGDLIV-FEIRANGFLYHMVRNIVGTLLEVG 202
Query: 315 QGLESIDVIESLLD 328
+G S + I+ +L+
Sbjct: 203 RGKLSPEDIKEILE 216
>gnl|CDD|211343 cd02866, PseudoU_synth_TruA_Archea, Archeal pseudouridine
synthases. This group consists of archeal pseudouridine
synthases.Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. This group of proteins make Psedouridine in
tRNAs.
Length = 219
Score = 149 bits (378), Expect = 1e-42
Identities = 74/249 (29%), Positives = 111/249 (44%), Gaps = 41/249 (16%)
Query: 96 LKVMYFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKGVSSVG 155
LK+ Y G F+GF ++ TVE E+ KALE+ ++ + + + GRTD+GV ++G
Sbjct: 1 LKIAYDGTNFHGFQRQPDV-RTVEGELIKALEELGII-ESRARLYSA--GRTDRGVHALG 56
Query: 156 QVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSPAPTDF 215
V+ E E ++N LPKDI V+ + P DF
Sbjct: 57 NVVVFET-----------------------EKEP-IPPMINAKLPKDIWVLAGAKVPEDF 92
Query: 216 SARFSCISREYKYFFWRENLNLSAMESAGKKFVGEHDFRNFCKMDAANVHNYKRHVTSFE 275
R + Y+Y + ++ AM+ A KK +G HDF NF K D R
Sbjct: 93 DPRRWAHRKYYRYNL-GSDYDVEAMKEAAKKLIGTHDFSNFSKRD-------GRKDPVRT 144
Query: 276 ISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIGQGLESIDVIESLLDTN----G 331
I IS G + I + G +FLW+ VR +V L +G+G + +E LLD G
Sbjct: 145 IERIEISENGEFI-TIDVVGESFLWNMVRRIVGALSEVGKGKRENEWVEKLLDGEFRPEG 203
Query: 332 IPRKPQYNM 340
+P P +
Sbjct: 204 VPPAPPEGL 212
>gnl|CDD|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/
PUS2 like. This group consists of eukaryotic
pseudouridine synthases similar to Saccharomyces
cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis
elegans Pus1p and human PUS1. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
No cofactors are required. S. cerevisiae Pus1p catalyzes
the formation of psi34 and psi36 in the
intron-containing tRNAIle, psi35 in the
intron-containing tRNATyr, psi27 and/or psi28 in several
yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear
RNA (U2 snRNA). The presence of the intron is required
for the formation of psi 34, 35 and 36. In addition S.
cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans
Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p
makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle,
psi 34/36 in tRNAIle and, psi 32 and potentially 67 in
tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are
highly phylogenetically conserved. Psi
26,27,28,34,35,36,65 and 67 in tRNAs are less highly
conserved. Mouse Pus1p regulates nuclear receptor
activity through pseudouridylation of Steroid Receptor
RNA Activator. Missense mutation in human PUS1 causes
mitochondrial myopathy and sideroblastic anemia (MLASA).
Length = 245
Score = 150 bits (380), Expect = 1e-42
Identities = 77/266 (28%), Positives = 118/266 (44%), Gaps = 29/266 (10%)
Query: 96 LKVMYFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADK----KESHYSRCGRTDKGV 151
L Y G ++G + T+E E+ +AL K + K+ +SR RTDKGV
Sbjct: 1 LLFGYCGTGYHGMQYNPGAYKTIEGELERALFKAGAISESNAGDPKKIGFSRAARTDKGV 60
Query: 152 SSVGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSPA 211
+ V++ L+ I + E + D V LN LP DIRV G +
Sbjct: 61 HAARNVVS--LKVIIDDP-------------EGLGILEDLVEKLNSHLPSDIRVFGITRV 105
Query: 212 PTDFSARFSCISREYKYFFWRENLN-LSAMESAGKKFVGEHDFRNFCKMDAANVHNYKRH 270
F+AR +C SR Y+Y L L K++VG H+F NF + R
Sbjct: 106 TKSFNARKACDSRTYEYLLPTFALETLQRFNEILKEYVGTHNFHNFTVKKKFEDPSANRF 165
Query: 271 VTSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIGQGLESIDVIESLLDT- 329
+ SF +S ++ EG + +IKI G +F+ HQ+R M+ + I +G +IE +
Sbjct: 166 IKSFYVSEPFVIEEGLEWISIKIHGQSFMLHQIRKMIGLAIAIVRGGAPESLIELSFNKD 225
Query: 330 --NGIPRKPQYNMAPEIPLVLQSCDF 353
IP +AP + L+L+ F
Sbjct: 226 KIIIIP------LAPGLGLLLERPHF 245
>gnl|CDD|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase. Involved
in the formation of pseudouridine at the anticodon stem
and loop of transfer-RNAs Pseudouridine is an isomer of
uridine (5-(beta-D-ribofuranosyl) uracil, and id the
most abundant modified nucleoside found in all cellular
RNAs. The TruA-like proteins also exhibit a conserved
sequence with a strictly conserved aspartic acid, likely
involved in catalysis.
Length = 103
Score = 89.8 bits (223), Expect = 5e-22
Identities = 36/111 (32%), Positives = 54/111 (48%), Gaps = 11/111 (9%)
Query: 245 KKFVGEHDFRNFCKMDAANVH-NYKRHVTSFEISPCYISFEGNQLCAIKIRGSAFLWHQV 303
K + G HDF F K V + R + S I +L +I+G+ FL+HQV
Sbjct: 3 KLYDGTHDFSGFQKQR--TVQKSLIRTIESIGI------ERDGELLVFEIKGNGFLYHQV 54
Query: 304 RCMVAVLFMIGQGLESIDVIESLLDTNGIPRKPQYNMAPEIPLVLQSCDFD 354
R MV L G+G+ +++ + SLL++ PR P AP + L L +D
Sbjct: 55 RIMVGALLRTGKGVHALEQVVSLLNSKLRPRAPPT--APAVGLYLFHVRYD 103
Score = 35.1 bits (81), Expect = 0.011
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 12/77 (15%)
Query: 96 LKVMYFGQ-RFYGFASDGNMEPTVESEIFKA--LEKTRLLVADKK---------ESHYSR 143
+Y G F GF ++ ++ I LLV + K
Sbjct: 1 AAKLYDGTHDFSGFQKQRTVQKSLIRTIESIGIERDGELLVFEIKGNGFLYHQVRIMVGA 60
Query: 144 CGRTDKGVSSVGQVIAI 160
RT KGV ++ QV+++
Sbjct: 61 LLRTGKGVHALEQVVSL 77
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional.
Length = 245
Score = 93.7 bits (233), Expect = 7e-22
Identities = 78/278 (28%), Positives = 106/278 (38%), Gaps = 50/278 (17%)
Query: 92 RYVALKVMYFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKGV 151
+ VA V Y G F+G+ ++ TV+ ALE+ K+ + GRTD GV
Sbjct: 2 KRVAAVVSYDGSNFFGYQGQPDVR-TVQGVFEDALERIF-----KQRIYTQAAGRTDTGV 55
Query: 152 SSVGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSPA 211
+ GQVIA N N M E D +N LP DI V
Sbjct: 56 HANGQVIAF---------NCPNDRM----------TEEDIKNAMNANLPDDIYVKKVFEV 96
Query: 212 PTDFSARFSCISREYKYF--------------FW--RENLNLSAMESAGKKFVGEHDFRN 255
P +F RF R Y YF W L+L AM A K GEHDF +
Sbjct: 97 PKNFHPRFDAKKRIYHYFILTSKEKNVFLRKYVWWFPYELDLEAMRKAAKYLEGEHDFTS 156
Query: 256 FCKMDAANVHNYKRHVTSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIGQ 315
F + N R + I + + + L I++ G +FL VR +V L +G
Sbjct: 157 FKTGS--DERNPVRTIYRIRI----LRLKKD-LILIRVEGRSFLRRMVRNIVGALVKVGL 209
Query: 316 GLESIDVIESLLDTNGIPRKPQYNMAPEIPLVLQSCDF 353
G + I+ +L+ R AP L L F
Sbjct: 210 GQWEPEKIKEVLEARD--RSKAAGTAPAHGLYLYKVLF 245
>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional.
Length = 272
Score = 91.1 bits (226), Expect = 1e-20
Identities = 80/283 (28%), Positives = 122/283 (43%), Gaps = 56/283 (19%)
Query: 92 RYVALKVMYFGQRFYG--FASDGNMEPTVESEIFKAL--EKTRLLVADKKESHYSRCGRT 147
R +AL + Y G F G + +DG ++AL E+ R+++A GRT
Sbjct: 2 RTIALLLEYDGTDFAGSQWQTDGRTVQGALEAAWQALTQERRRIVLA----------GRT 51
Query: 148 DKGVSSVGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIG 207
D GV + GQV ++++ T+ T+ R LN LP+DI V
Sbjct: 52 DAGVHARGQV------AHVQ---TDTRHSLATI-----------WRGLNAHLPEDIGVQN 91
Query: 208 WSPAPTDFSARFSCISREYKYFF----------------WRENLNLSAMESAGKKFVGEH 251
AP DF ARFS I REY+Y + L+++AM++A K +G H
Sbjct: 92 AWEAPPDFHARFSAIQREYRYVIDCAPAPSPQLRHQVLHYAGTLDVAAMDAALKLLIGTH 151
Query: 252 DFRNFCKMDAANVHNYKRHVTSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLF 311
DF F A + R + F G L AI++ +AFL H VR +V L
Sbjct: 152 DFAAFT--TAPQEGSTVRTCYWARCT-DTEWF-GRPLLAIEVAANAFLQHMVRNIVGTLL 207
Query: 312 MIGQGLESIDVIESLLDTNGIPRKPQYNMAPEIPLVLQSCDFD 354
++G+G ++D ++L R+ AP L L + +
Sbjct: 208 LVGRGRMTVDQFGAVL--ASRDRRLAGPTAPAHGLYLTAVRYP 248
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed.
Length = 245
Score = 88.3 bits (219), Expect = 6e-20
Identities = 69/254 (27%), Positives = 106/254 (41%), Gaps = 50/254 (19%)
Query: 92 RYVALKVMYFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKGV 151
R + L + Y G R+ G+ GN + T++ +I L + +E CGRTD GV
Sbjct: 2 RNIKLTIQYDGSRYKGWQKLGNNDNTIQGKIESVLSEMT-----GEEIEIIGCGRTDAGV 56
Query: 152 SSVGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEI-DYVRVLNRVLPKDIRVIGWSP 210
++ QV +N + E+ ED+I Y LN LP DI V
Sbjct: 57 HALNQV------ANFQ------------TDEKLSEDKIKKY---LNEYLPNDIVVTNVEE 95
Query: 211 APTDFSARFSCISREYKYFFW----------------RENLNLSAMESAGKKFVGEHDFR 254
F AR++ S+ Y Y W E L++ AM+ A K VG HDF
Sbjct: 96 VDERFHARYNVKSKTYLYKIWNEKFHNVFMRKYSMHVNEKLDVKAMKEAAKYLVGSHDFT 155
Query: 255 NFCKMDAANVHNYKRHVTSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIG 314
+F + R + S +I E + I++ G+ FL + VR +V L +G
Sbjct: 156 SFTNAKSKKKSTV-REIYSIDI------MEEDGFVQIRVSGNGFLHNMVRIIVGALIEVG 208
Query: 315 QGLESIDVIESLLD 328
G + I+ +L+
Sbjct: 209 LGQLKAEDIKQILE 222
>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 56.1 bits (135), Expect = 2e-08
Identities = 53/196 (27%), Positives = 78/196 (39%), Gaps = 54/196 (27%)
Query: 91 KRYVALKVMYFGQRFYGF------ASDGNMEPTVESEIFKALEKTRLLVADKKESHY--- 141
K+ V L+V Y G + G +S +E +E+ IFKA +ES+Y
Sbjct: 70 KKKVVLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKA--------GGIRESNYGNL 121
Query: 142 -----SRCGRTDKGVSSVGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYV---R 193
+R RTDKGV S+ +I S+ + E +D+ D + +
Sbjct: 122 HKIGWARSSRTDKGVHSLATMI----------------SLKMEIPENAWKDDPDGIALAK 165
Query: 194 VLNRVLPKDIRVIGWSPAPTDFSARFSCISREYKYFFWRENL-------------NLSAM 240
+N LP +IRV PA F R C R+Y Y E + ++S
Sbjct: 166 FINSHLPDNIRVFSILPAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFSSEEIDEHISEF 225
Query: 241 ESAGKKFVGEHDFRNF 256
S F GEH F N+
Sbjct: 226 NSILNGFEGEHPFHNY 241
Score = 29.1 bits (65), Expect = 5.5
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 283 FEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIGQGLESIDVIE 324
G + I G +F+ HQ+R MV + + L D+I
Sbjct: 351 SLGFDFVELSIWGESFMLHQIRKMVGTAVAVKRELLPRDIIR 392
>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional.
Length = 256
Score = 52.5 bits (126), Expect = 1e-07
Identities = 61/265 (23%), Positives = 94/265 (35%), Gaps = 64/265 (24%)
Query: 97 KVMYFGQRFYGFASDGN-MEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKGVSSVG 155
++ Y G FYGF N +EP + + L R RTD GVS+VG
Sbjct: 6 RIAYDGTLFYGFTGHPNSLEPALRRVFGEIL---------------GRGSRTDPGVSAVG 50
Query: 156 QVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSPAPTDF 215
V+ + + N+ LP+ + + P F
Sbjct: 51 NVVMTSQKLPLGYVNSK--------------------------LPRGVWAWAVAEVPEGF 84
Query: 216 SARFSCISREYKYF--FWRENLNLSAMESAGKKFVGEHDFRNFCKMDAANVHNYKRH--- 270
+ R R Y Y W E++ AM A + G HD+ +F + ++
Sbjct: 85 NPR-RAKRRRYLYVAPHWGEDVE--AMREAAELLAGTHDYSSFIQRRG------EKATPT 135
Query: 271 -VTSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIGQGLESIDVIESLLDT 329
T +EI + G+ L + G F +R M + G+G+ S I LL+
Sbjct: 136 VTTVYEIG---VELRGD-LIYLYFVGRGFRNKMIRKMAWAILAAGRGVLSRRDIAELLER 191
Query: 330 NGIPRKPQYNMAPEIPLVLQSCDFD 354
PR AP LVL ++D
Sbjct: 192 ---PRPGAVPSAPAEGLVLLDIEYD 213
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 34.9 bits (80), Expect = 0.056
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 3 EAKQELI---SSLQSQLEALQNRVKELEADNAKLLSKLSL--CRCEKIEDKVHDGVEDGT 57
+ K+EL+ L+++ E +Q R+K LE +N++L L ++ + D +E G
Sbjct: 149 KEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKLPGEVYDLKKRW-DELEPGV 207
Query: 58 TLVEENRKTE 67
L EE ++
Sbjct: 208 ELPEEELISD 217
>gnl|CDD|192486 pfam10224, DUF2205, Predicted coiled-coil protein (DUF2205).
This entry represent a highly conserved 100 residue
region which is likely to be a coiled-coil structure.
The exact function is unknown.
Length = 80
Score = 31.3 bits (71), Expect = 0.16
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 3 EAKQELIS---SLQSQLEALQNRVKELEADNAKLLS 35
EA+Q LI LQ LE L RV+ ++ +N KL S
Sbjct: 16 EARQRLIEQALELQDSLEDLSQRVEAVKEENLKLRS 51
>gnl|CDD|197390 cd10155, BsYrkD-like_DUF156, Uncharacterized protein YrkD from
Bacillus subtilis and related domains; this domain
superfamily was previously known as part of DUF156.
This domain family contains an uncharacterized protein
YrkD from Bacillus subtilis and related proteins. This
family is part of a larger superfamily that contains
various transcriptional regulators that respond to
different stressors such as Cu(I), Ni(I), sulfite, and
formaldehyde, and includes CsoRs (copper-sensitive
operon repressors). CsoRs form homotetramers (dimer of
dimers). In Mycobacterium tuberculosis CsoR, within each
dimer, two Cys residues on opposite subunits, along with
a His residue, bind the Cu(I) ion (forming a triagonal
S2N coordination complex, C-H-C). These residues are
conserved in the majority of members of this
superfamily. In this family, however, not all these
residues are conserved, there is an Asn instead of the
His (C-N-C); also a conserved Tyr and a Glu residue that
facilitates allosteric regulation of DNA binding for
CsoRs are very poorly conserved.
Length = 82
Score = 29.9 bits (68), Expect = 0.49
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 152 SSVGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYV 192
SSV + I + + N++EC GE QEE+I++ I+ +
Sbjct: 40 SSVDRAIGLIVAENLEECVREEEEDGED-QEEKIQEAINLL 79
>gnl|CDD|233065 TIGR00634, recN, DNA repair protein RecN. All proteins in this
family for which functions are known are ATP binding
proteins involved in the initiation of recombination and
recombinational repair [DNA metabolism, DNA replication,
recombination, and repair].
Length = 563
Score = 32.4 bits (74), Expect = 0.49
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 2 SEAKQEL--ISSLQSQLEALQNRVKELEADNAKLLSKLSLCR---CEKIEDKVH 50
+ K+EL + LEAL+ V +LE + K LSL R E++ +V
Sbjct: 332 EKIKEELDQLDDSDESLEALEEEVDKLEEELDKAAVALSLIRRKAAERLAKRVE 385
>gnl|CDD|188167 TIGR01780, SSADH, succinate-semialdehyde dehydrogenase. Succinic
semialdehyde dehydrogenase is one of three enzymes
constituting 4-aminobutyrate (GABA) degradation in both
prokaryotes and eukaryotes, catalyzing the
(NAD(P)+)-dependent catabolism reaction of succinic
semialdehyde to succinate for metabolism by the citric
acid cycle. The EC number depends on the cofactor:
1.2.1.24 for NAD only, 1.2.1.79 for NADP only, and
1.2.1.16 if both can be used. In Escherichia coli,
succinic semialdehyde dehydrogenase is located in an
unidirectionally transcribed gene cluster encoding
enzymes for GABA degradation and is suggested to be
cotranscribed with succinic semialdehyde transaminase
from a common promoter upstream of SSADH. Similar gene
arrangements can be found in characterized Ralstonia
eutropha and the genome analysis of Bacillus subtilis.
Prokaryotic succinic semialdehyde dehydrogenases
(1.2.1.16) share high sequence homology to characterized
succinic semialdehyde dehydrogenases from rat and human
(1.2.1.24), exhibiting conservation of proposed cofactor
binding residues, and putative active sites (G-237 &
G-242, C-293 & G-259 respectively of rat SSADH).
Eukaryotic SSADH enzymes exclusively utilize NAD+ as a
cofactor, exhibiting little to no NADP+ activity. While
a NADP+ preference has been detected in prokaryotes in
addition to both NADP+- and NAD+-dependencies as in
E.coli, Pseudomonas, and Klebsiella pneumoniae. The
function of this alternative SSADH currently is unknown,
but has been suggested to play a possible role in
4-hydroxyphenylacetic degradation. Just outside the
scope of this model, are several sequences belonging to
clades scoring between trusted and noise. These
sequences may be actual SSADH enzymes, but lack
sufficiently close characterized homologs to make a
definitive assignment at this time. SSADH enzyme belongs
to the aldehyde dehydrogenase family (pfam00171),
sharing a common evolutionary origin and enzymatic
mechanism with lactaldehyde dehydrogenase. Like in
lactaldehyde dehydrogenase and succinate semialdehyde
dehydrogenase, the mammalian catalytic glutamic acid and
cysteine residues are conserved in all the enzymes of
this family (PS00687, PS00070) [Central intermediary
metabolism, Other].
Length = 448
Score = 32.0 bits (73), Expect = 0.70
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 42 CEKIEDKVHDGVEDGTTLVEENRKTESGG 70
EK+E + D VE G +V ++ E GG
Sbjct: 309 VEKVEKHIADAVEKGAKVVTGGKRHELGG 337
>gnl|CDD|110536 pfam01539, HCV_env, Hepatitis C virus envelope glycoprotein E1.
Length = 190
Score = 31.0 bits (70), Expect = 0.72
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 6/38 (15%)
Query: 371 HLRNECQ----VYQLQAAIFHEALLNCLPLANDQNSLR 404
H+ N+C +QL A+ H C+P + N+ R
Sbjct: 10 HVTNDCSNSSITWQLADAVLH--TPGCVPCEREGNTSR 45
>gnl|CDD|202837 pfam03980, Nnf1, Nnf1. NNF1 is an essential yeast gene that is
necessary for chromosome segregation. It is associated
with the spindle poles and forms part of a kinetochore
subcomplex called MIND.
Length = 108
Score = 29.9 bits (68), Expect = 0.93
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 8 LISSLQSQLEALQNRVKELEADNAKLLSKLS 38
L+ L QL+ L R+++++A+NA L ++
Sbjct: 73 LVPYLLKQLDELNARLQKIQAENAALADEIQ 103
>gnl|CDD|191111 pfam04849, HAP1_N, HAP1 N-terminal conserved region. This family
represents an N-terminal conserved region found in
several huntingtin-associated protein 1 (HAP1)
homologues. HAP1 binds to huntingtin in a polyglutamine
repeat-length-dependent manner. However, its possible
role in the pathogenesis of Huntington's disease is
unclear. This family also includes a similar N-terminal
conserved region from hypothetical protein products of
ALS2CR3 genes found in the human juvenile amyotrophic
lateral sclerosis critical region 2q33-2q34.
Length = 307
Score = 31.3 bits (71), Expect = 1.0
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 3 EAKQELISSLQSQLEALQNRVKELEADNAKL 33
E +QE I+ L SQ+ LQ + K +N +L
Sbjct: 231 ERQQEEITHLLSQIVDLQKKCKSYALENEEL 261
Score = 29.8 bits (67), Expect = 3.1
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 6/46 (13%)
Query: 15 QLEALQNRVKELEADNAKLLSKLSLCRCEKI--EDK----VHDGVE 54
QLEALQ ++K LE +N L S+ S + E + E+K V+D V+
Sbjct: 162 QLEALQEKLKLLEEENEHLRSEASHLKTETVTYEEKEQQLVNDCVK 207
>gnl|CDD|148617 pfam07111, HCR, Alpha helical coiled-coil rod protein (HCR). This
family consists of several mammalian alpha helical
coiled-coil rod HCR proteins. The function of HCR is
unknown but it has been implicated in psoriasis in
humans and is thought to affect keratinocyte
proliferation.
Length = 739
Score = 31.6 bits (71), Expect = 1.0
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 1 MSEAKQELISSLQSQLEALQNRVKELEADNAKLLSKLSLCRCE-----KIEDKVHDGVED 55
+++A E +SSL+S+ E L+ ++ LE A L+ + E + K + +E
Sbjct: 156 LTQAHLEALSSLRSKAEGLEKSLQSLETRRAGEAKALAAAQAEADTLREQLSKTQEELEA 215
Query: 56 GTTLVEENRK 65
TLVE+ RK
Sbjct: 216 QVTLVEQLRK 225
>gnl|CDD|221084 pfam11336, DUF3138, Protein of unknown function (DUF3138). This
family of proteins with unknown function appear to be
restricted to Proteobacteria.
Length = 514
Score = 31.4 bits (71), Expect = 1.1
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 1 MSEAKQELISSLQSQLEALQNRVKELEA 28
+ + I +LQ+QL ALQ +V EL A
Sbjct: 19 AAASDASQIKALQAQLTALQQQVNELRA 46
>gnl|CDD|219737 pfam08172, CASP_C, CASP C terminal. This domain is the C-terminal
region of the CASP family of proteins. It is a Golgi
membrane protein which is thought to have a role in
vesicle transport.
Length = 245
Score = 30.4 bits (69), Expect = 1.4
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 11/43 (25%)
Query: 6 QEL---ISSLQSQLEALQNRVKELEADNAKLLSKLSLCRCEKI 45
EL + + +L+ ++ L+ADN KL EKI
Sbjct: 96 TELEEELRKQNQTISSLRRELESLKADNIKL--------YEKI 130
>gnl|CDD|220640 pfam10234, Cluap1, Clusterin-associated protein-1. This protein is
conserved from worms to humans. The protein of 413 amino
acids contains a central coiled-coil domain, possibly
the region that binds to clusterin. Cluap1 expression is
highest in the nucleus and gradually increases during
late S to G2/M phases of the cell cycle and returns to
the basal level in the G0/G1 phases. In addition, it is
upregulated in colon cancer tissues compared to
corresponding non-cancerous mucosa. It thus plays a
crucial role in the life of the cell.
Length = 269
Score = 30.7 bits (70), Expect = 1.4
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 6 QELISSLQSQLEALQNRVKELEADNAKLLSKL 37
+E I +L ++L+ LQ + L++D A L +K+
Sbjct: 170 KEAIKNLAARLQQLQAELDNLKSDEANLEAKI 201
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 30.1 bits (68), Expect = 1.5
Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 1 MSEAKQELISSLQSQLEALQNRVKELEADNAKLLSKLSLCRCEKIE 46
+SE KQ+L S LQ +LE L+ R+ ELE++ L L L R
Sbjct: 81 LSELKQQL-SELQEELEDLEERIAELESELEDLKEDLQLLRELLKS 125
>gnl|CDD|226400 COG3883, COG3883, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 30.5 bits (69), Expect = 1.5
Identities = 9/32 (28%), Positives = 21/32 (65%)
Query: 6 QELISSLQSQLEALQNRVKELEADNAKLLSKL 37
Q I SL +Q+E +Q+++ EL+ + + +++
Sbjct: 51 QNEIESLDNQIEEIQSKIDELQKEIDQSKAEI 82
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 30.0 bits (68), Expect = 1.8
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 6/68 (8%)
Query: 3 EAKQELISSLQSQLEALQNRVKELEADNAKLLSKLS-----LCRCEKIEDKVHDGVEDGT 57
E +QEL + LQ +L LQ ++ EL+ +N +L +LS L R +K ++ +
Sbjct: 70 ELQQEL-AELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAI 128
Query: 58 TLVEENRK 65
L EENR+
Sbjct: 129 ELDEENRE 136
Score = 28.4 bits (64), Expect = 5.4
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 11 SLQSQLEALQNRVKELEADNAKLLSKLSLCRCEKIEDKVHDGVEDGTTLVEENRKTES 68
S + +L LQ + EL+ + A+L +L+ + E E K ++ +TL E + +
Sbjct: 63 SARERLPELQQELAELQEELAELQEQLAELQQENQELK-----QELSTLEAELERLQK 115
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 30.6 bits (69), Expect = 2.1
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 8/80 (10%)
Query: 9 ISSLQSQLEALQNRVKELEADNAKLLSKLSLCRC-------EKIEDKVHDGVEDGTTLVE 61
+SSL ++ AL+ + EL N ++L+ S+C EK ++ E + L E
Sbjct: 425 VSSLNQRIRALRENLDELS-RNMEMLNGQSVCPVCGTTLGEEKSNHIINHYNEKKSRLEE 483
Query: 62 ENRKTESGGCKTGKKKVKEK 81
+ R+ E +K V K
Sbjct: 484 KIREIEIEVKDIDEKIVDLK 503
>gnl|CDD|238046 cd00094, HX, Hemopexin-like repeats.; Hemopexin is a heme-binding
protein that transports heme to the liver.
Hemopexin-like repeats occur in vitronectin and some
matrix metalloproteinases family (matrixins). The HX
repeats of some matrixins bind tissue inhibitor of
metalloproteinases (TIMPs). This CD contains 4 instances
of the repeat.
Length = 194
Score = 29.6 bits (67), Expect = 2.1
Identities = 16/60 (26%), Positives = 21/60 (35%), Gaps = 6/60 (10%)
Query: 200 PKDIRVIGWSPAPTDFSARFSCISREYKYFF-----WRENLNLSAMESAGKKFVGEHDFR 254
PK I +G+ P A YFF WR + M+ K + E DF
Sbjct: 86 PKPISDLGFPPTVKQIDAALRWPDNGKTYFFKGDKYWRYDEKTQKMDPGYPKLI-ETDFP 144
>gnl|CDD|225747 COG3206, GumC, Uncharacterized protein involved in
exopolysaccharide biosynthesis [Cell envelope
biogenesis, outer membrane].
Length = 458
Score = 30.1 bits (68), Expect = 2.7
Identities = 10/38 (26%), Positives = 24/38 (63%)
Query: 1 MSEAKQELISSLQSQLEALQNRVKELEADNAKLLSKLS 38
++ +++++SL ++L L+ + LE + A+L +LS
Sbjct: 329 IAAELRQILASLPNELALLEQQEAALEKELAQLKGRLS 366
>gnl|CDD|197664 smart00338, BRLZ, basic region leucin zipper.
Length = 65
Score = 27.1 bits (61), Expect = 3.0
Identities = 9/29 (31%), Positives = 21/29 (72%)
Query: 13 QSQLEALQNRVKELEADNAKLLSKLSLCR 41
++++E L+ +V++LEA+N +L ++ R
Sbjct: 25 KAEIEELERKVEQLEAENERLKKEIERLR 53
>gnl|CDD|201054 pfam00170, bZIP_1, bZIP transcription factor. The Pfam entry
includes the basic region and the leucine zipper
region.
Length = 64
Score = 27.3 bits (61), Expect = 3.1
Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 2/40 (5%)
Query: 13 QSQLEALQNRVKELEADNAKLLSKLSLCR--CEKIEDKVH 50
++ +E L+ +VKELEA+N L S+L + C K++ +
Sbjct: 25 KAYIEELEEKVKELEAENKTLRSELERLKKECAKLKSENE 64
>gnl|CDD|219934 pfam08614, ATG16, Autophagy protein 16 (ATG16). Autophagy is a
ubiquitous intracellular degradation system for
eukaryotic cells. During autophagy, cytoplasmic
components are enclosed in autophagosomes and delivered
to lysosomes/vacuoles. ATG16 (also known as Apg16) has
been shown to be bind to Apg5 and is required for the
function of the Apg12p-Apg5p conjugate in the yeast
autophagy pathway.
Length = 194
Score = 29.4 bits (66), Expect = 3.1
Identities = 10/36 (27%), Positives = 24/36 (66%)
Query: 1 MSEAKQELISSLQSQLEALQNRVKELEADNAKLLSK 36
+E Q+ + SL +L AL+ ++++L+ +N +L+ +
Sbjct: 145 DNETLQDELISLNIELNALEEKLRKLQKENQELVER 180
>gnl|CDD|234405 TIGR03936, sam_1_link_chp, radical SAM-linked protein. This model
describes an uncharacterized protein encoded adjacent
to, or as a fusion protein with, an uncharacterized
radical SAM protein.
Length = 209
Score = 29.1 bits (66), Expect = 3.4
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 183 EQIEDEIDYVRVLNRVLPKDIRVIGWSPAPTDFSARFSCISR-EYKYFF 230
+ D + + LN VLP+ I V+ P + + I +Y+
Sbjct: 69 TEEIDPEEVLERLNAVLPEGIEVLEVEEVPDKAPSLMALIDAADYRITL 117
>gnl|CDD|203738 pfam07716, bZIP_2, Basic region leucine zipper.
Length = 54
Score = 26.8 bits (60), Expect = 3.6
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 17 EALQNRVKELEADNAKLLSKLSLCRCE 43
E L+ RVKELE +NA+L K+ E
Sbjct: 28 EELEERVKELEEENAQLRQKVEQLEKE 54
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 29.7 bits (68), Expect = 3.9
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 1 MSEAKQEL---ISSLQSQLEALQNRVKELEADNAKLLSKLSLCRCEKIEDKVHD 51
+ E L S L ++EAL +KELE + +L +KL+ + + +
Sbjct: 703 LKELAALLKAKPSELPERVEALLEELKELEKELEQLKAKLAAAAAGDLLAQAKE 756
>gnl|CDD|100091 cd03089, PMM_PGM, The phosphomannomutase/phosphoglucomutase
(PMM/PGM) bifunctional enzyme catalyzes the reversible
conversion of 1-phospho to 6-phospho-sugars (e.g.
between mannose-1-phosphate and mannose-6-phosphate or
glucose-1-phosphate and glucose-6-phosphate) via a
bisphosphorylated sugar intermediate. The reaction
involves two phosphoryl transfers, with an intervening
180 degree reorientation of the reaction intermediate
during catalysis. Reorientation of the intermediate
occurs without dissociation from the active site of the
enzyme and is thus, a simple example of processivity, as
defined by multiple rounds of catalysis without release
of substrate. Glucose-6-phosphate and
glucose-1-phosphate are known to be utilized for energy
metabolism and cell surface construction, respectively.
PMM/PGM belongs to the alpha-D-phosphohexomutase
superfamily which includes several related enzymes that
catalyze a reversible intramolecular phosphoryl transfer
on their sugar substrates. Other members of this
superfamily include phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the
phosphoglucomutases (PGM1 and PGM2). Each of these
enzymes has four domains with a centrally located active
site formed by four loops, one from each domain. All
four domains are included in this alignment model.
Length = 443
Score = 29.4 bits (67), Expect = 4.2
Identities = 20/58 (34%), Positives = 23/58 (39%), Gaps = 28/58 (48%)
Query: 66 TESGG----CKTG----KKKVKEK-------MSGTLNHHFKRYVALKVMYFGQRFYGF 108
E+GG KTG K K+KE MSG H F F R+YGF
Sbjct: 286 EEAGGKPIMWKTGHSFIKAKMKETGALLAGEMSG---HIF----------FKDRWYGF 330
>gnl|CDD|163064 TIGR02894, DNA_bind_RsfA, transcription factor, RsfA family. In a
subset of endospore-forming members of the Firmcutes,
members of this protein family are found, several to a
genome. Two very strongly conserved sequences regions
are separated by a highly variable linker region. Much
of the linker region was excised from the seed alignment
for this model. A characterized member is the
prespore-specific transcription RsfA from Bacillus
subtilis, previously called YwfN, which is controlled by
sigma factor F and seems to fine-tune expression of some
genes in the sigma-F regulon. A paralog in Bacillus
subtilis is designated YlbO [Regulatory functions, DNA
interactions, Cellular processes, Sporulation and
germination].
Length = 161
Score = 28.6 bits (64), Expect = 4.5
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 12 LQSQLEALQNRVKELEADNAKLLSKLS 38
L++Q E+LQ R +ELE + KL +LS
Sbjct: 109 LKNQNESLQKRNEELEKELEKLRQRLS 135
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 29.3 bits (66), Expect = 4.6
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 3 EAKQELISSLQSQLEALQNRVKELEADNAKLLSKLS 38
E E + L+ QLE L++R+KELE + A+L +L
Sbjct: 442 EELNEELEELEEQLEELRDRLKELERELAELQEELQ 477
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 29.3 bits (66), Expect = 4.6
Identities = 10/31 (32%), Positives = 22/31 (70%)
Query: 3 EAKQELISSLQSQLEALQNRVKELEADNAKL 33
E +++ ++ L S+L A Q +++EL A+ ++L
Sbjct: 206 EERKKTLAQLNSELSADQKKLEELRANESRL 236
>gnl|CDD|218532 pfam05276, SH3BP5, SH3 domain-binding protein 5 (SH3BP5). This
family consists of several eukaryotic SH3 domain-binding
protein 5 or c-Jun N-terminal kinase (JNK)-interacting
proteins (SH3BP5 or Sab). Sab binds to and serves as a
substrate for JNK in vitro, and has been found to
interact with the Src homology 3 (SH3) domain of
Bruton's tyrosine kinase (Btk). Inspection of the
sequence of Sab reveals the presence of two putative
mitogen-activated protein kinase interaction motifs
(KIMs) similar to that found in the JNK docking domain
of the c-Jun transcription factor, and four potential
serine-proline JNK phosphorylation sites in the
C-terminal half of the molecule.
Length = 240
Score = 29.0 bits (65), Expect = 4.9
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 2 SEAKQELISSLQSQLEALQNRVKELEAD--NAKLLSKLSLCRCEKIEDKVH 50
S EL QLE + V+ELEA AK +L E+I +++H
Sbjct: 172 SRPYFELKQVYTQQLEIQKLLVQELEAKVAQAKASYSTALRNLEQISERIH 222
>gnl|CDD|223258 COG0180, TrpS, Tryptophanyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 314
Score = 28.7 bits (65), Expect = 6.3
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 3 EAKQELISSLQSQLEALQNRVKELEAD 29
E K+EL ++Q L+ +Q R +EL D
Sbjct: 274 ECKKELAEAIQEFLKPIQERREELRED 300
>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein. This domain is found in
cell division proteins which are required for
kinetochore-spindle association.
Length = 321
Score = 28.5 bits (64), Expect = 6.7
Identities = 25/91 (27%), Positives = 38/91 (41%), Gaps = 17/91 (18%)
Query: 2 SEAKQEL------ISSLQSQLEALQNRVKELEADNAKLLSKLSLCRCEKIEDKVHDGVED 55
+A+QEL IS + QLE LQ ++EL L +K S E + +
Sbjct: 210 EKARQELRSLSVKISEKRKQLEELQQELQELTIAIEALTNKKSELLEE---------IAE 260
Query: 56 GTTLVEENRKTESGGCKTGKKKVK--EKMSG 84
+ EE R + K KV +K++G
Sbjct: 261 AEKIREECRGWSAKEISKLKAKVSLLQKLTG 291
>gnl|CDD|218051 pfam04380, BMFP, Membrane fusogenic activity. BMFP consists of
two structural domains, a coiled-coil C-terminal domain
via which the protein self-associates as a trimer, and
an N-terminal domain disordered at neutral pH but
adopting an amphipathic alpha-helical structure in the
presence of phospholipid vesicles, high ionic strength,
acidic pH or SDS. BMFP interacts with phospholipid
vesicles though the predicted amphipathic alpha-helix
induced in the N-terminal half of the protein and
promotes aggregation and fusion of vesicles in vitro.
Length = 79
Score = 26.3 bits (59), Expect = 9.1
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 3 EAKQELISSLQSQLEALQNRVKELEA 28
+ ++ +++ + +LEAL+ RV LEA
Sbjct: 53 DVQRAVLARTREKLEALEARVAALEA 78
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 28.5 bits (64), Expect = 9.6
Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 8/86 (9%)
Query: 5 KQELISSLQSQLEALQNRVKELEADNAKLLSKLS-----LCRCEKIEDKVHDGVEDGTTL 59
K EL SS+ S++EAL+ +KE L +++ L ++ + +
Sbjct: 200 KSELPSSILSEIEALEAELKEQSEKYEDLAQEIAHLRNELEEAQRSLESLEKKFRSEGGD 259
Query: 60 VEENR---KTESGGCKTGKKKVKEKM 82
+ E R + + + +K + ++
Sbjct: 260 LFEEREQLERQLKEIEAARKANRAQL 285
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 28.3 bits (64), Expect = 9.6
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 11/86 (12%)
Query: 3 EAKQEL--ISSLQSQLEALQNRVKELEADNAKLLSKLSLCRC---EKIEDKVHD-----G 52
+ K+EL + + + LEAL+ VK+L+A+ + LS R +++E +V
Sbjct: 329 KIKEELAQLDNSEESLEALEKEVKKLKAELLEAAEALSAIRKKAAKELEKEVTAELKALA 388
Query: 53 VEDGTTLVEENRKTESGGCKTGKKKV 78
+E VE E G KV
Sbjct: 389 MEKARFTVELK-PLEESPTADGADKV 413
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.134 0.394
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,587,459
Number of extensions: 2066767
Number of successful extensions: 2466
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2397
Number of HSP's successfully gapped: 88
Length of query: 437
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 337
Effective length of database: 6,502,202
Effective search space: 2191242074
Effective search space used: 2191242074
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.8 bits)