RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3554
(672 letters)
>gnl|CDD|203323 pfam05739, SNARE, SNARE domain. Most if not all vesicular membrane
fusion events in eukaryotic cells are believed to be
mediated by a conserved fusion machinery, the SNARE
[soluble N-ethylmaleimide-sensitive factor (NSF)
attachment protein (SNAP) receptors] machinery. The
SNARE domain is thought to act as a protein-protein
interaction module in the assembly of a SNARE protein
complex.
Length = 62
Score = 64.1 bits (157), Expect = 4e-13
Identities = 19/52 (36%), Positives = 35/52 (67%)
Query: 306 RADTMQNIESTIVELGGIFQQLAHMVQEQEEMVERIDANILDTELHVESAHR 357
R + ++ +ES+I EL +F + V+EQ E+++RID N+ +T+ VE A++
Sbjct: 1 RDEALEELESSIGELKQLFLDMGEEVEEQGELLDRIDDNVDNTQSRVERANK 52
>gnl|CDD|201451 pfam00804, Syntaxin, Syntaxin. Syntaxins are the prototype family
of SNARE proteins. They usually consist of three main
regions - a C-terminal transmembrane region, a central
SNARE domain which is characteristic of and conserved in
all syntaxins (pfam05739), and an N-terminal domain that
is featured in this entry. This domain varies between
syntaxin isoforms; in syntaxin 1A it is found as three
alpha-helices with a left-handed twist. It may fold back
on the SNARE domain to allow the molecule to adopt a
'closed' configuration that prevents formation of the
core fusion complex - it thus has an auto-inhibitory
role. The function of syntaxins is determined by their
localisation. They are involved in neuronal exocytosis,
ER-Golgi transport and Golgi-endosome transport, for
example. They also interact with other proteins as well
as those involved in SNARE complexes. These include
vesicle coat proteins, Rab GTPases, and tethering
factors.
Length = 103
Score = 62.8 bits (153), Expect = 3e-12
Identities = 33/109 (30%), Positives = 54/109 (49%), Gaps = 13/109 (11%)
Query: 101 EFMLIAKTIGKNISSTYAKLEKLTLLAKRKSLFND----KPTEIQELTYIIKEDLNSLNQ 156
EF + I + I LE+L L KR D E++ELT IK+ ++ +
Sbjct: 4 EFFDEVEEIREEIQKIRQNLEELQKLHKRILTAPDSDKELREELEELTQEIKQLARAIKK 63
Query: 157 QIAKLQQVGKHQRDVISSGHQHLLSHSSSVVLALQSKLASMSTEFKNVL 205
++ LQQ+ K + L HSS+V +++LA++S +FK+VL
Sbjct: 64 KLKSLQQLNK---------SEQGLGHSSAVDRIRKNQLANLSKKFKDVL 103
>gnl|CDD|238115 cd00193, t_SNARE, Soluble NSF (N-ethylmaleimide-sensitive fusion
protein)-Attachment protein (SNAP) REceptor domain;
these alpha-helical motifs form twisted and parallel
heterotetrameric helix bundles; the core complex
contains one helix from a protein that is anchored in
the vesicle membrane (synaptobrevin), one helix from a
protein of the target membrane (syntaxin), and two
helices from another protein anchored in the target
membrane (SNAP-25); their interaction forms a core which
is composed of a polar zero layer, a flanking
leucine-zipper layer acts as a water tight shield to
isolate ionic interactions in the zero layer from the
surrounding solvent.
Length = 60
Score = 60.2 bits (147), Expect = 1e-11
Identities = 18/55 (32%), Positives = 37/55 (67%)
Query: 303 IQSRADTMQNIESTIVELGGIFQQLAHMVQEQEEMVERIDANILDTELHVESAHR 357
Q R + ++ +E++I EL IF L V+EQ E+++RI+ N+ + +++V+ A++
Sbjct: 1 EQERDEELEQLEASIGELKQIFLDLGTEVEEQGELLDRIEDNVDNADVNVKRANK 55
>gnl|CDD|197699 smart00397, t_SNARE, Helical region found in SNAREs. All
alpha-helical motifs that form twisted and parallel
four-helix bundles in target soluble
N-ethylmaleimide-sensitive factor (NSF) attachment
protein (SNAP) receptor proteins. This motif found in
"Q-SNAREs".
Length = 66
Score = 59.1 bits (144), Expect = 2e-11
Identities = 16/61 (26%), Positives = 37/61 (60%)
Query: 297 DQSEQFIQSRADTMQNIESTIVELGGIFQQLAHMVQEQEEMVERIDANILDTELHVESAH 356
Q+ + R + ++ +E +I EL IF + ++EQ E ++RI+ N+ D +++++ A+
Sbjct: 1 QQALAREEERDEELEQLEKSIQELKQIFLDMGTELEEQGEQLDRIEDNVDDADVNLKKAN 60
Query: 357 R 357
+
Sbjct: 61 K 61
>gnl|CDD|227635 COG5325, COG5325, t-SNARE complex subunit, syntaxin [Intracellular
trafficking and secretion].
Length = 283
Score = 57.9 bits (140), Expect = 5e-09
Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 2/90 (2%)
Query: 274 EDQNMSDTALQQQQQQKTMMLYEDQSEQ--FIQSRADTMQNIESTIVELGGIFQQLAHMV 331
ED+ + QQ Q+ + E+ Q I R + ++N+ I EL IF+ L +V
Sbjct: 159 EDEESLSSLGSQQTLQQQGLSNEELEYQQILITERDEEIKNLARGIYELNEIFRDLGSLV 218
Query: 332 QEQEEMVERIDANILDTELHVESAHRDQNI 361
EQ E+V+RID NI +T ++++A+++
Sbjct: 219 GEQGELVDRIDFNIENTSDNLKNANKELEK 248
Score = 29.0 bits (65), Expect = 8.2
Identities = 10/62 (16%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 398 KSETYTEIDANILDTELHVESAHREILKYFQSV-TSNRWLMIKIFAVLIFFFIFFVVFLA 456
+ E ID NI +T ++++A++E+ K + + + +L+ ++
Sbjct: 221 QGELVDRIDFNIENTSDNLKNANKELEKAPAHQRRTKKCRFYLLLILLVVLLFVSLIKKL 280
Query: 457 HN 458
+
Sbjct: 281 RS 282
>gnl|CDD|227406 COG5074, COG5074, t-SNARE complex subunit, syntaxin [Intracellular
trafficking and secretion].
Length = 280
Score = 49.1 bits (117), Expect = 3e-06
Identities = 19/58 (32%), Positives = 33/58 (56%)
Query: 303 IQSRADTMQNIESTIVELGGIFQQLAHMVQEQEEMVERIDANILDTELHVESAHRDQN 360
+Q+R ++ IE T+ EL +F + +V EQ+E V+ ID N+ D + +VE +
Sbjct: 180 VQARHQEIKKIEKTMAELTQLFNDMEELVIEQQENVDVIDKNVEDAQENVEQGVGHTD 237
>gnl|CDD|151935 pfam11498, Activator_LAG-3, Transcriptional activator LAG-3. The
C.elegans Notch pathway, involved in the control of
growth, differentiation and patterning in animal
development, relies on either of the receptors GLP-1 or
LIN-12. Both these receptors promote signalling by the
recruitment of LAG-3 to target promoters, where it then
acts as a transcriptional activator. LAG-3 works as a
ternary complex together with the DNA binding protein,
LAG-1.
Length = 476
Score = 38.4 bits (88), Expect = 0.012
Identities = 30/117 (25%), Positives = 45/117 (38%), Gaps = 31/117 (26%)
Query: 221 QYSGGGAPSSLPPAAMSGPHHQGSVLLADEQCAIDMSDTALQQQQQQKTMMLYEDQNMSD 280
+ G P S PP AM+ H Q QQQ M L + Q M
Sbjct: 302 EAGGDRMPQSAPPPAMNPQHIA-------------------QLAQQQNKMRLLQQQEMEM 342
Query: 281 TALQQQQQQKTMMLYEDQSEQFIQSRADTMQNIESTIVELGGIFQQLAHMVQEQEEM 337
++QQ+QQ+ M ++ Q +Q Q + +Q QQ H +Q+ +M
Sbjct: 343 QRIEQQRQQQIMHQHQQQQQQEHQQQQMLLQQ------------QQQMHQLQQHHQM 387
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 35.7 bits (82), Expect = 0.087
Identities = 25/150 (16%), Positives = 41/150 (27%), Gaps = 11/150 (7%)
Query: 228 PSSLPPAAMSGPHHQGSVLLADE--QCAIDMSDTALQQQQQQKTMMLYEDQNMSDTALQQ 285
AA GPH V Q M ++ Q Q QQ M + A
Sbjct: 121 GQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQGQAGGM 180
Query: 286 QQQQKTMMLYEDQSEQFIQSRADTMQNIESTIVELGGIFQQLAHMVQEQEEMVERID-AN 344
Q Q+ + + + G + QQ Q+Q+ + N
Sbjct: 181 NQGQQGPVGQQQPPQMGQPGMPGGGGQ--------GQMQQQGQPGGQQQQNPQMQQQLQN 232
Query: 345 ILDTELHVESAHRDQNICISTKTQAHGDQN 374
++ + D + + Q G
Sbjct: 233 QQQQQMDQQQGPADAQAQMGQQQQGQGGMQ 262
Score = 34.6 bits (79), Expect = 0.18
Identities = 22/114 (19%), Positives = 32/114 (28%), Gaps = 4/114 (3%)
Query: 225 GGAPSSLPPAAMSGPHHQGSVLLADEQCAIDMSDTALQQQQQQKTMMLYEDQNMSDTALQ 284
G P M P + + Q + + QQQ M + Q
Sbjct: 300 PGGGQGGPGQPMGPPPQRPGAVPQGGQA---VQQGVMSAGQQQLKQMKLRNMRGQQQTQQ 356
Query: 285 QQQQQKTMMLYEDQSEQFIQ-SRADTMQNIESTIVELGGIFQQLAHMVQEQEEM 337
QQQQQ Q + Q + M + ++ M Q Q M
Sbjct: 357 QQQQQGGNHPAAHQQQMNQQVGQGGQMVALGYLNIQGNQGGLGANPMQQGQPGM 410
Score = 33.8 bits (77), Expect = 0.35
Identities = 20/116 (17%), Positives = 36/116 (31%), Gaps = 9/116 (7%)
Query: 224 GGGAPSSLPPAAMSGPHHQGSVLLADEQCAIDMSDTALQQQQQQKTMMLYED-----QNM 278
GG A + ++ Q + + + A + Q QQ + + M
Sbjct: 144 GGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQGQAGG--MNQGQQGPVGQQQPPQMGQPGM 201
Query: 279 SDTALQQQQQQKTMMLYEDQSEQFIQSRADTMQNIESTIVELGGIFQQLAHMVQEQ 334
Q Q QQ+ + Q +Q + + + G A M Q+Q
Sbjct: 202 PGGGGQGQMQQQGQPGGQQQQNPQMQ--QQLQNQQQQQMDQQQGPADAQAQMGQQQ 255
Score = 30.4 bits (68), Expect = 3.6
Identities = 16/78 (20%), Positives = 23/78 (29%)
Query: 212 LKQAKSRRDQYSGGGAPSSLPPAAMSGPHHQGSVLLADEQCAIDMSDTALQQQQQQKTMM 271
+ G P G Q V+ A +Q M ++ QQQ +
Sbjct: 299 MPGGGQGGPGQPMGPPPQRPGAVPQGGQAVQQGVMSAGQQQLKQMKLRNMRGQQQTQQQQ 358
Query: 272 LYEDQNMSDTALQQQQQQ 289
+ N QQ QQ
Sbjct: 359 QQQGGNHPAAHQQQMNQQ 376
>gnl|CDD|113902 pfam05149, Flagellar_rod, Paraflagellar rod protein. This family
consists of several eukaryotic paraflagellar rod
component proteins. The eukaryotic flagellum represents
one of the most complex macromolecular structures found
in any organism and contains more than 250 proteins. In
addition to its locomotive role, the flagellum is
probably involved in nutrient uptake since receptors for
host low-density lipoproteins are localised on the
flagellar membrane as well as on the flagellar pocket
membrane.
Length = 289
Score = 34.6 bits (80), Expect = 0.12
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 282 ALQQQQQQKTMMLYEDQSEQFIQSRADTMQNIESTIVELGGIFQQLAHMVQEQEEMVER 340
+Q+K +SE+F+Q + Q I EL ++L + +E+ E VER
Sbjct: 33 DAADAKQRKRYSAQRRESEKFLQQNVEQQQACWRAIQEL---ERELRDLAEERREEVER 88
>gnl|CDD|224176 COG1256, FlgK, Flagellar hook-associated protein [Cell motility and
secretion].
Length = 552
Score = 34.7 bits (80), Expect = 0.18
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 12/71 (16%)
Query: 106 AKTIGKNISSTYAKLEKLTLLAKRKSLFNDKPTEIQELTYIIKEDLNSLNQQIAKLQQVG 165
A+T+ I++TY +L L RK + + + E+ ++K+ + LN+QI K++ G
Sbjct: 140 AQTLVNQINNTYEQLTDL-----RKDINAEIAATVDEVNSLLKQ-IADLNKQIRKVKAAG 193
Query: 166 KH------QRD 170
QRD
Sbjct: 194 NDPNDLLDQRD 204
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 33.5 bits (76), Expect = 0.39
Identities = 39/235 (16%), Positives = 83/235 (35%), Gaps = 25/235 (10%)
Query: 108 TIGKNISSTYAKLEKL--TLLAKRKSLFNDKPTEIQELTYIIKEDLNSLNQQIAKLQQVG 165
+ +N+ S +L+ + L A R L + +E S Q+ + ++
Sbjct: 64 LLNRNLRSGVFQLDDIRPQLRALRTEL--GTAQGEKRAAETEREAARSELQKARQEREAV 121
Query: 166 KHQRDVISSGH---QHLLSHSSSVVLALQSKLASMSTEFKNVLEVRTENLKQAKSRRDQY 222
+ + Q L+ + LQ++L +++ + + LE + ++L QA ++ Q
Sbjct: 122 RQELAAARQNLAKAQQELARLTKQAQDLQTRLKTLAEQRRQ-LEAQAQSL-QASQKQLQ- 178
Query: 223 SGGGAPSSLPPAAMSGPHHQGSVLLADEQCAIDMSDTALQQQQQQKTMMLYEDQNMSDTA 282
+ + L + L I+ L + E + A
Sbjct: 179 ---ASATQLKSQVLD---------LKLRSAQIEQEAQNLATRANAAQARTEELARRAAAA 226
Query: 283 LQQQQQQKTMMLYEDQSEQFIQSRADTMQNIESTIVELGGIFQQLAHMVQEQEEM 337
Q Q + Q Q I +RA+ ++ E +L + A + QE ++
Sbjct: 227 QQTAQAIQQRDAQISQKAQQIAARAEQIRERER---QLQRLETAQARLEQEVAQL 278
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 33.3 bits (77), Expect = 0.44
Identities = 13/55 (23%), Positives = 20/55 (36%), Gaps = 5/55 (9%)
Query: 262 QQQQQQKTM-----MLYEDQNMSDTALQQQQQQKTMMLYEDQSEQFIQSRADTMQ 311
Q + Q+ M L E Q +SD + Q+Q E Q +Q +
Sbjct: 582 GQSEMQQAMEGLGETLREQQGLSDETFRDLQEQFNAQRGEQQGQQGQGGQGQGQP 636
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family protein.
[Transport and binding proteins, Other].
Length = 1394
Score = 33.2 bits (76), Expect = 0.59
Identities = 13/32 (40%), Positives = 14/32 (43%)
Query: 424 LKYFQSVTSNRWLMIKIFAVLIFFFIFFVVFL 455
L+ S S RW IF IFF I VF
Sbjct: 1355 LEPISSKYSGRWRNFGIFIAFIFFNIIATVFF 1386
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 33.1 bits (76), Expect = 0.66
Identities = 24/106 (22%), Positives = 54/106 (50%), Gaps = 7/106 (6%)
Query: 119 KLEKLTLLAKRKSLFNDKPTEIQELTYIIKEDLNSLNQQIAKLQQVGKHQRDVISSGHQH 178
E+L L +R + + +++E + ED+ SL +I +L++ + + S +
Sbjct: 822 LRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEE----LIEELESELEA 877
Query: 179 LLSHSSSVVLAL---QSKLASMSTEFKNVLEVRTENLKQAKSRRDQ 221
LL+ +S+ AL +S+L +S E + + R+E ++ + R++
Sbjct: 878 LLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELREK 923
Score = 32.0 bits (73), Expect = 1.2
Identities = 35/231 (15%), Positives = 80/231 (34%), Gaps = 25/231 (10%)
Query: 118 AKLEKLTLLAKRKSLFNDKPTEIQELTYIIKEDLNSLNQQIAKLQQVGKH---QRDVISS 174
EKL L S ++ E+Q+ Y + +++ L QQ L++ + Q + + +
Sbjct: 264 ELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEA 323
Query: 175 GHQHLLSHSSSVVLALQSKLASMSTEFKNVLEVRTENLKQAKSRRDQYSGGGAPSSLPPA 234
+ L S L +LA + + + + E + + +
Sbjct: 324 QLEELESKL----DELAEELAELEEKLEELKEELESLEAELEELEAEL----------EE 369
Query: 235 AMSGPHHQGSVLLADEQCAIDMSDTALQQQQQQKTMMLYEDQ-NMSDTALQQQQQQKTMM 293
S L E ++ LQ + E + + ++ QQ+ +
Sbjct: 370 LESRLEELEEQL---ETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEEL 426
Query: 294 LYEDQSEQFIQSRADTMQNIESTIVELGGIFQQLAHMVQEQEEMVERIDAN 344
L + + + + +E EL + ++L + + EE+ E ++
Sbjct: 427 LKKLEEAEL----KELQAELEELEEELEELQEELERLEEALEELREELEEA 473
>gnl|CDD|220306 pfam09599, IpaC_SipC, Salmonella-Shigella invasin protein C
(IpaC_SipC). This entry represents a family of proteins
associated with bacterial type III secretion systems,
which are injection machines for virulence factors into
host cell cytoplasm. Characterized members of this
protein family are known to be secreted and are
described as invasins, including IpaC from Shigella
flexneri and SipC from Salmonella typhimurium. Members
may be referred to as invasins, pathogenicity island
effectors, and cell invasion proteins.
Length = 337
Score = 32.2 bits (73), Expect = 0.76
Identities = 36/208 (17%), Positives = 65/208 (31%), Gaps = 26/208 (12%)
Query: 113 ISSTYAKLEKLTLLAKRKSLFNDKPTEIQELTYIIKEDLNSLNQQIA-KLQQVGKHQRDV 171
I+ AKL+ L + +L + +L+ + LN Q A KL +
Sbjct: 144 ITGVGAKLQAKGLSKQSGALKKNLKP-SNKLSAEAAQLKLQLNGQNAPKLVADELKHVKI 202
Query: 172 ISSGHQHLLSHSSSVVLALQSKLASMSTEFKNVLEVRTENLKQAKSR------RDQYSGG 225
+ + + + ++S E K L R E+L Q K
Sbjct: 203 KRTTGD---ATKMLQKNKITASNKALSAEHKAQLSQRVESL-QDKIDLHQQAYEQNTLKA 258
Query: 226 GAPSSLPPAAMSGPHHQGSVLLADEQCAIDMSDTALQQQQQQKTMMLYEDQNMSDTALQQ 285
A + M A ++S + Q Q+ Q S TA
Sbjct: 259 QAMQMIGDLIMRM-----------SANAGNISGGSGQYAATQEEAEQQISQASSRTASTA 307
Query: 286 QQQQKTMMLYEDQSEQFIQSRADTMQNI 313
+ + +++Q IQ +++I
Sbjct: 308 SNETREAS---RKTKQLIQELLKILESI 332
>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 = 31.9 bits (73), Expect = 0.88
Identities = 19/107 (17%), Positives = 42/107 (39%), Gaps = 9/107 (8%)
Query: 120 LEKLTLLAKRKSLFNDKPTEIQELTYIIKEDLNSLNQQIAKLQQVGK----HQRDVISSG 175
E L + + + L N I + +++ L +L ++IA L+Q+ +
Sbjct: 153 EENLEGMKRDEELLNKDLNLINSIKPKLRKKLQALKEEIASLRQLADELNLCDPLELEKA 212
Query: 176 HQHLLSHSSSVVLALQSKLASMSTEFKNVLEVRTENLKQAKSRRDQY 222
Q L S S + S+ E + L+ T ++ +++ +
Sbjct: 213 RQELRSLSVKI-----SEKRKQLEELQQELQELTIAIEALTNKKSEL 254
>gnl|CDD|224241 COG1322, COG1322, Predicted nuclease of restriction
endonuclease-like fold, RmuC family [General function
prediction only].
Length = 448
Score = 32.4 bits (74), Expect = 0.89
Identities = 22/138 (15%), Positives = 46/138 (33%), Gaps = 11/138 (7%)
Query: 256 MSDTALQQQQQQKTMMLYED----QNMSDTALQQQQQQKTMMLYEDQSEQFIQSRADTM- 310
T + Q ++ E + LQ ++Q + ++ Q Q A+ +
Sbjct: 56 QLRTFARSLQALNLELIQELNELKARLQQQLLQSREQLQLLIESLAQLSSEFQELANEIF 115
Query: 311 QNIESTIVELGG-IFQQLAHMVQEQEE-----MVERIDANILDTELHVESAHRDQNICIS 364
+ + + EL +QL ++E E + +RI + + +E R
Sbjct: 116 EELNRRLAELNQQNLKQLLKPLREVLEKFREQLEQRIHESAEERSTLLEEIDRLLGEIQQ 175
Query: 365 TKTQAHGDQNTWISTKTQ 382
+A KT+
Sbjct: 176 LAQEAGNLTAALKGNKTR 193
>gnl|CDD|236942 PRK11637, PRK11637, AmiB activator; Provisional.
Length = 428
Score = 32.4 bits (74), Expect = 0.93
Identities = 44/211 (20%), Positives = 77/211 (36%), Gaps = 78/211 (36%)
Query: 147 IKEDLNSLNQQIAKLQQVGKHQRDVIS------------SGHQHLLSHSSSV----VLAL 190
+ + ++ LN IAKL+Q Q +++ +G Q +LS S +LA
Sbjct: 101 LNKQIDELNASIAKLEQQQAAQERLLAAQLDAAFRQGEHTGLQLILSGEESQRGERILAY 160
Query: 191 QSKLASMSTEFKNVLEVRTENLKQAKSRRDQYSGGGAPSSLPPAAMSGPHHQGSVLLADE 250
L + R E + + K R++ LA +
Sbjct: 161 FGYLN----------QARQETIAELKQTREE-------------------------LAAQ 185
Query: 251 QCAIDMSDTALQQQQQQKTMMLYEDQNMSDTALQQQQQQKTMMLYEDQSEQFIQSRADTM 310
+ L+++Q Q+ +LYE QQ QQQK EQ R T+
Sbjct: 186 K-------AELEEKQSQQKTLLYE---------QQAQQQKL--------EQARNERKKTL 221
Query: 311 QNIESTIVELGGIFQQLAHMVQEQEEMVERI 341
+ES++ + QQL+ + + + + I
Sbjct: 222 TGLESSLQKDQ---QQLSELRANESRLRDSI 249
>gnl|CDD|217411 pfam03185, CaKB, Calcium-activated potassium channel, beta subunit.
Length = 201
Score = 31.6 bits (72), Expect = 0.99
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 582 HVISQLVTPQWIFCTNTPRS--WRQGKVPALRYFIFLPTSPKKKSLIWH 628
V++ +T +W C+ T S + P L+ F+ L + +++L+ H
Sbjct: 53 TVLNTNITDEWFNCSFTCGSDCRGVSQYPCLQVFVNL-SHSGRRALLHH 100
>gnl|CDD|236526 PRK09458, pspB, phage shock protein B; Provisional.
Length = 75
Score = 29.5 bits (67), Expect = 1.0
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 324 FQQLAHMVQEQEEMVERIDA--NILDTE 349
Q+LA + ++ E M ERI A ILD E
Sbjct: 41 QQRLAQLTEKAERMRERIQALEAILDAE 68
>gnl|CDD|224427 COG1510, COG1510, Predicted transcriptional regulators
[Transcription].
Length = 177
Score = 31.2 bits (71), Expect = 1.0
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 72 VIRSLQGKNIVRAVAAKDVRRAQF--VQNYGEFM--LIAKTIGKNISSTYAKLEKL 123
++ LQ N+V+ V K R+ F +++ + L + + I T L+KL
Sbjct: 61 GLKKLQDWNLVKKVFEKGDRKDYFEAEKDFSQIFRTLFEEKWKREIDPTKEALKKL 116
>gnl|CDD|236356 PRK08944, motB, flagellar motor protein MotB; Reviewed.
Length = 302
Score = 31.1 bits (71), Expect = 1.8
Identities = 13/70 (18%), Positives = 30/70 (42%)
Query: 249 DEQCAIDMSDTALQQQQQQKTMMLYEDQNMSDTALQQQQQQKTMMLYEDQSEQFIQSRAD 308
+ Q S QQQ+ ++ + ++ A Q+Q + + Q E+ I+ A
Sbjct: 105 EFQAGESDSAGGTQQQRGKQRGGEASAEVKAEKAAAQEQIEDLVKKLAQQLEKEIEDGAI 164
Query: 309 TMQNIESTIV 318
++++ I+
Sbjct: 165 EIESLGQQII 174
>gnl|CDD|236412 PRK09204, secY, preprotein translocase subunit SecY; Reviewed.
Length = 426
Score = 30.9 bits (71), Expect = 2.1
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 423 ILKYFQSVTSNRWLMIKIFAVLIFFFIFFVVFLAHN 458
I Y L I ++A+LI FF FF + N
Sbjct: 299 IANYLSP---GSPLYILLYALLIIFFTFFYTAIQFN 331
>gnl|CDD|239330 cd03032, ArsC_Spx, Arsenate Reductase (ArsC) family, Spx subfamily;
Spx is a unique RNA polymerase (RNAP)-binding protein
present in bacilli and some mollicutes. It inhibits
transcription by binding to the C-terminal domain of the
alpha subunit of RNAP, disrupting complex formation
between RNAP and certain transcriptional activator
proteins like ResD and ComA. In response to oxidative
stress, Spx can also activate transcription, making it a
general regulator that exerts both positive and negative
control over transcription initiation. Spx has been
shown to exert redox-sensitive transcriptional control
over genes like trxA (TRX) and trxB (TRX reductase),
genes that function in thiol homeostasis. This
redox-sensitive activity is dependent on the presence of
a CXXC motif, present in some members of the Spx
subfamily, that acts as a thiol/disulfide switch. Spx
has also been shown to repress genes in a
sulfate-dependent manner independent of the presence of
the CXXC motif.
Length = 115
Score = 29.5 bits (67), Expect = 2.2
Identities = 15/68 (22%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 273 YEDQNMSDTALQQQQQQKTMMLYEDQSEQFIQSRADTMQNIESTIVELGGIFQQLAHMVQ 332
+E++N+ L +++ ++ + L E+ E I +R+ +N+ I EL +L ++
Sbjct: 27 FEERNLFKQPLTKEELKEILSLTENGVEDIISTRSKAFKNLNIDIDELS--LSELIRLIS 84
Query: 333 EQEEMVER 340
E ++ R
Sbjct: 85 EHPSLLRR 92
>gnl|CDD|140267 PTZ00240, PTZ00240, 60S ribosomal protein P0; Provisional.
Length = 323
Score = 30.7 bits (69), Expect = 2.3
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 82 VRAVAAKDVRRAQFVQNYGEFMLIAKTIGKNISSTYAKLEKLTLLAKRKSLFNDKPTEIQ 141
VR+ DVRRA ++ EF++ KT+ I A+ +K + AK LFND+ E
Sbjct: 33 VRSQQVHDVRRA--LRGKAEFVMGKKTLQAKIVEKRAQAKKASAEAK---LFNDQCEEKN 87
Query: 142 ELT 144
L+
Sbjct: 88 LLS 90
>gnl|CDD|143806 pfam00015, MCPsignal, Methyl-accepting chemotaxis protein (MCP)
signalling domain. This domain is thought to transduce
the signal to CheA since it is highly conserved in very
diverse MCPs.
Length = 213
Score = 30.1 bits (68), Expect = 2.8
Identities = 22/114 (19%), Positives = 51/114 (44%), Gaps = 10/114 (8%)
Query: 234 AAMSGPHHQGSVLLADEQCAIDMSDTALQQQQQQK--TMMLYEDQNMSDTALQQQQQQKT 291
AA +G +G ++ADE + A + Q K ++ E ++ + QQ +T
Sbjct: 67 AARAGEQGRGFAVVADE-----VRKLAERSAQAAKEIEALIEEIVKQTNDSTASIQQTRT 121
Query: 292 MMLYEDQSEQFIQSRADTMQNIESTIVELGGIFQQLAHMVQEQEEMVERIDANI 345
+ + ++S + ++ I + E+ I Q++A EQ +++++ +
Sbjct: 122 EV---EVGSTIVESTGEALKEIVDAVAEIADIVQEIAAASDEQSAGIDQVNQAV 172
>gnl|CDD|192566 pfam10392, COG5, Golgi transport complex subunit 5. The COG
complex, the peripheral membrane oligomeric protein
complex involved in intra-Golgi protein trafficking,
consists of eight subunits arranged in two lobes bridged
by Cog1. Cog5 is in the smaller, B lobe, bound in with
Cog6-8, and is itself bound to Cog1 as well as,
strongly, to Cog7.
Length = 132
Score = 29.2 bits (66), Expect = 3.0
Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 6/48 (12%)
Query: 161 LQQVGKHQRDVISSGHQHLLSH------SSSVVLALQSKLASMSTEFK 202
+Q++ + R +I+S H LLSH +SS++ L+S L +S ++
Sbjct: 42 IQELDRRIRTLITSNHLELLSHLSSIKSASSILSTLKSSLEYLSASYE 89
>gnl|CDD|233214 TIGR00967, 3a0501s007, preprotein translocase, SecY subunit.
Members of this protein family are the SecY component of
the SecYEG translocon, or protein translocation pore,
which is driven by the ATPase SecA. This model does not
discriminate bacterial from archaeal forms [Protein
fate, Protein and peptide secretion and trafficking].
Length = 410
Score = 30.3 bits (69), Expect = 3.4
Identities = 11/40 (27%), Positives = 21/40 (52%)
Query: 423 ILKYFQSVTSNRWLMIKIFAVLIFFFIFFVVFLAHNCKNI 462
L S++ + + ++ +LI FF FF V L N +++
Sbjct: 282 FLNPILSLSLSDPIGAILYLILIIFFSFFYVELQLNPEDM 321
>gnl|CDD|204766 pfam11877, DUF3397, Protein of unknown function (DUF3397). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 114 to 128 amino acids in
length.
Length = 116
Score = 28.7 bits (65), Expect = 3.7
Identities = 8/36 (22%), Positives = 13/36 (36%)
Query: 423 ILKYFQSVTSNRWLMIKIFAVLIFFFIFFVVFLAHN 458
IL F + W + + F I V F++
Sbjct: 18 ILVKFFRLKRRGWAFLAAVDLATPFLIIAVHFISKV 53
>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein. Members of
this family are long (~850 residue) bacterial proteins
from the alpha Proteobacteria. Each has 2-3 predicted
transmembrane helices near the N-terminus and a long
C-terminal region that includes stretches of
Gln/Gly-rich low complexity sequence, predicted by TMHMM
to be outside the membrane. In Bradyrhizobium japonicum,
two tandem reading frames are together homologous the
single members found in other species; the cutoffs
scores are set low enough that the longer scores above
the trusted cutoff and the shorter above the noise
cutoff for this model.
Length = 851
Score = 30.3 bits (68), Expect = 3.9
Identities = 22/114 (19%), Positives = 42/114 (36%), Gaps = 19/114 (16%)
Query: 246 LLADEQCAIDMSDTALQQQQQQKTMMLYEDQNMSDTALQQQQQQKTMMLYE--------D 297
L + A+ L QQ + L + + L+QQ Q M E D
Sbjct: 528 LTDKLRAAMQTYMRQLAQQLRNNPQQLARPLDPNTKVLRQQDLQNMMDQIENLARSGDRD 587
Query: 298 QSEQFIQSRADTMQNIESTIVELG-------GIFQQ----LAHMVQEQEEMVER 340
Q++Q + M N++ G G +Q L ++++Q+++ +
Sbjct: 588 QAKQLLSQLQQMMNNLQMGQPGQGQQMGDQSGDMEQQMNKLGELMRKQQQLRDE 641
>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 30.2 bits (68), Expect = 4.0
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 101 EFMLIAKTIGKNISSTYAKLEKLTLLAKRKSLFNDKPTEIQELTYIIKEDLNSLNQQIAK 160
++ IAK +G N+ T +E + + AK+ S + + + +K L S Q+I K
Sbjct: 448 NYIKIAKALGINLEKT---IEAMRIFAKKYSSYAEIGRMLGTWNSSVKIILESNTQEIEK 504
Query: 161 LQQVGKHQRDVI 172
L+++ K + +I
Sbjct: 505 LEEIRKIELKLI 516
>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional.
Length = 1047
Score = 30.2 bits (68), Expect = 4.3
Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 12/69 (17%)
Query: 242 QGSVLLADE---------QCAIDMSDTALQQQQQQKTMMLYEDQNMSDTALQQQQQQKTM 292
G LL E Q D L QQQQ+ + + + LQQ+ ++
Sbjct: 208 SGVALLTPEQVQSLTASLQVLTDEEKQLLTAQQQQQQSLNWLTRL---DELQQEASRRQQ 264
Query: 293 MLYEDQSEQ 301
L + + +
Sbjct: 265 ALQQALAAE 273
>gnl|CDD|204784 pfam11932, DUF3450, Protein of unknown function (DUF3450). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are about 260 amino acids in
length.
Length = 250
Score = 29.5 bits (67), Expect = 4.8
Identities = 13/88 (14%), Positives = 39/88 (44%), Gaps = 4/88 (4%)
Query: 259 TALQQQQQQKTMMLYED-QNMSDTALQQQQQQKTMMLYEDQSEQFIQSRADTMQNIESTI 317
A Q Q+K + Q + Q ++ + + +Y DQ ++ + ++ + +++ I
Sbjct: 35 VAAAAQSQKKIDKWADQTQELLAEIRQLLKEIENLRVYNDQLQRLVANQQQEIASLQQQI 94
Query: 318 VELGGIFQQLAHMVQEQEEMVERIDANI 345
++ Q L ++ M++ ++ +
Sbjct: 95 EQIEKTRQGLVPLM---YRMIDGLEQFV 119
>gnl|CDD|182398 PRK10350, PRK10350, hypothetical protein; Provisional.
Length = 145
Score = 28.8 bits (64), Expect = 5.7
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 259 TALQQQQQQKTMMLYEDQNMSDTALQQQQQQKTM 292
T +Q QQ Q+ ML + + T LQQQ Q +
Sbjct: 41 TQMQTQQIQQKGMLNQQLK-TQTRLQQQHLQNQI 73
>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III
C-methyltransferase; Provisional.
Length = 390
Score = 29.3 bits (66), Expect = 6.4
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 1/53 (1%)
Query: 241 HQGSVLLADEQCAIDMSDTALQQQQQQKTMMLYEDQNMSDTALQQ-QQQQKTM 292
Q + A+ TALQ+ Q+ + L AL Q +QQ +
Sbjct: 59 KQQAQNQTATNDALANQLTALQKAQESQKQELEGILKQQAKALDQANRQQAAL 111
>gnl|CDD|223910 COG0840, Tar, Methyl-accepting chemotaxis protein [Cell motility
and secretion / Signal transduction mechanisms].
Length = 408
Score = 29.6 bits (66), Expect = 6.6
Identities = 10/38 (26%), Positives = 22/38 (57%)
Query: 308 DTMQNIESTIVELGGIFQQLAHMVQEQEEMVERIDANI 345
++ I + I E+ + ++A +EQ ++E I+A+I
Sbjct: 331 SSLGEIAAAIEEVSQLISEIAAATEEQTAVLEEINASI 368
>gnl|CDD|179855 PRK04460, PRK04460, nickel responsive regulator; Provisional.
Length = 137
Score = 28.4 bits (64), Expect = 6.8
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 143 LTYIIKEDLNSLNQQIAKLQQVGKHQRDVISSGHQHLLSHSSSVVLALQSK 193
+T + ++ L Q++ ++Q H ++ISS H HL H+ VL L+ K
Sbjct: 57 VTLVYNHHVSDLAQKLTEIQH--DHHDEIISSLHVHLDHHNCLEVLVLKGK 105
>gnl|CDD|114219 pfam05483, SCP-1, Synaptonemal complex protein 1 (SCP-1).
Synaptonemal complex protein 1 (SCP-1) is the major
component of the transverse filaments of the
synaptonemal complex. Synaptonemal complexes are
structures that are formed between homologous
chromosomes during meiotic prophase.
Length = 787
Score = 29.7 bits (66), Expect = 6.8
Identities = 39/218 (17%), Positives = 96/218 (44%), Gaps = 16/218 (7%)
Query: 135 DKPTEIQELTYIIKEDLNSLNQQIAKLQQVGKHQRDVISSGHQHLLSHSSSVVLALQSKL 194
+K ++++LT++++E + NQ K + ++ +++I HL + ++LQ +
Sbjct: 251 EKENKMKDLTFLLEESRDKANQLEEKTKLQDENLKELIEKKD-HLTKELEDIKMSLQRSM 309
Query: 195 ASMSTEFKNVLEVRTENLKQ----AKSRRDQYSGGGAPSSLPPAAMSGPHHQGSVLLADE 250
++ + L++ T+ + Q +++ ++ + A S LL E
Sbjct: 310 STQKA-LEEDLQIATKTICQLTEEKEAQMEELNKAKAAHSFVVTEFEATTCSLEELLRTE 368
Query: 251 QCAIDMSDTALQ---QQQQQKTMMLYEDQNMSDTALQQQQQQKTMMLYEDQSEQFIQSRA 307
Q ++ ++ L+ + Q+K+ L E + + ++ K +L ED +
Sbjct: 369 QQRLEKNEDQLKIITMELQKKSSELEEMTKFKNNKEVELEELKK-ILAED------EKLL 421
Query: 308 DTMQNIESTIVELGGIFQQLAHMVQEQEEMVERIDANI 345
D + E EL G Q+L ++Q +E+ + ++ +
Sbjct: 422 DEKKQFEKIAEELKGKEQELIFLLQAREKEIHDLEIQL 459
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 29.7 bits (67), Expect = 6.9
Identities = 19/105 (18%), Positives = 34/105 (32%), Gaps = 7/105 (6%)
Query: 121 EKLTLLAKRKSLFNDKPTEIQE----LTYIIKEDLNSLNQQIAKLQQVGKHQRDVISSGH 176
+L + R K ++Q L IKE L + + K + R+
Sbjct: 359 SELEEVEARLDALTGKHQDVQRKYERLKQKIKEQLE---RDLEKNNERLAAIREEKDRQK 415
Query: 177 QHLLSHSSSVVLALQSKLASMSTEFKNVLEVRTENLKQAKSRRDQ 221
+ ++ L+ +L + EF L + K R D
Sbjct: 416 AAIEEDLQALESQLRQQLEAGKLEFNEEEYELELRLGRLKQRLDS 460
>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 257 to 277 amino acids in length. This domain is
found associated with pfam00004. This domain has a
conserved LER sequence motif.
Length = 276
Score = 29.0 bits (65), Expect = 7.2
Identities = 23/103 (22%), Positives = 44/103 (42%), Gaps = 9/103 (8%)
Query: 262 QQQQQQKTMMLYEDQ---NMSDTALQQQQQQKTMMLYEDQSEQFIQSRADTMQNIESTIV 318
+Q QQ++ Y+D+ L+QQ++Q +L + Q E ++ A E I+
Sbjct: 100 EQTQQEQQRAQYQDELARKRYQKELEQQRRQNEELL-KMQEESVLRQEAMRRAT-EEEIL 157
Query: 319 ELGGIFQQLAH-MVQEQEEMVERIDANILDTELHVESAHRDQN 360
E+ + + E+E + +I+A E + D N
Sbjct: 158 EMR--RETIEEEAELERENIRAKIEAE-ARGRAKEERENEDIN 197
>gnl|CDD|217686 pfam03713, DUF305, Domain of unknown function (DUF305). Domain
found in small family of bacterial secreted proteins
with no known function. Also found in Paramecium
bursaria chlorella virus 1. This domain is short and
found in one or two copies. The domain has a conserved
HH motif that may be functionally important. This domain
belongs to the ferritin superfamily. It contains two
sequence similar repeats each of which is composed of
two alpha helices.
Length = 150
Score = 28.4 bits (64), Expect = 7.3
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 15/60 (25%)
Query: 234 AAMSGPHHQGSVLLADEQCAIDMSDTALQQQQQQKTMMLYEDQNMSDTALQQQQQQKTMM 293
A PHHQ A++M++ AL++ Q E + ++ + QQ + M
Sbjct: 5 AQDMIPHHQQ---------AVEMAELALERSQDP------EVRALAQDIIAAQQPEIGQM 49
>gnl|CDD|183426 PRK12309, PRK12309, transaldolase/EF-hand domain-containing
protein; Provisional.
Length = 391
Score = 28.9 bits (65), Expect = 8.9
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 403 TEIDANI-LDTELHVESAHREILKYFQSVTSNRWLMIKI 440
TE+DA + DTE + A + I Y + S ++IKI
Sbjct: 99 TEVDARLSYDTEATIAKARKLISLYEDAGISRDRVLIKI 137
>gnl|CDD|164794 PHA00369, H, minor spike protein.
Length = 325
Score = 28.8 bits (64), Expect = 8.9
Identities = 38/188 (20%), Positives = 72/188 (38%), Gaps = 25/188 (13%)
Query: 250 EQCAIDMSDTALQQ--QQQQKTMMLYEDQNMSDTALQQQQQQKTMMLYEDQSEQFIQSRA 307
E+ S ++ QK + + N + A Q QK + IQS A
Sbjct: 131 ERAGAGASSAGMEDAGFNNQKELTKMQLDNQKEIAKMQNDTQKQI--------AGIQS-A 181
Query: 308 DTMQNIESTIVELGGIFQQLAHMVQEQEEMVERIDANILDTELHVESAHRDQNICISTKT 367
+ QN + + ++ Q + Q+E R+ + + +T+L + + + T+
Sbjct: 182 TSRQNTKDS------VYAQNEMLQYNQKESQARVASILENTDLTKQQQTSEIMRQMLTQA 235
Query: 368 QAHG-----DQNTWISTKTQACEDTVRVTVPNKKYKSETYTEIDANILDTELHVESAHRE 422
Q G DQ ++ K A D V N +Y S +++ A D + A
Sbjct: 236 QTTGQHFTNDQIMELTRKVYAEIDKVHQDTQNSRYGS---SQVGATAKDVSNMITDAASG 292
Query: 423 ILKYFQSV 430
I+ +F+ +
Sbjct: 293 IVDWFRGI 300
>gnl|CDD|217986 pfam04247, SirB, Invasion gene expression up-regulator, SirB. SirB
up-regulates Salmonella typhimurium invasion gene
transcription. It is, however, not essential for the
expression of these genes. Its function is unknown.
Length = 122
Score = 27.5 bits (62), Expect = 9.4
Identities = 5/31 (16%), Positives = 11/31 (35%)
Query: 428 QSVTSNRWLMIKIFAVLIFFFIFFVVFLAHN 458
Q + WL KI ++ + + +
Sbjct: 63 QYPFVDPWLTEKILGLVAYIVLGVIALRGRT 93
>gnl|CDD|218813 pfam05929, Phage_GPO, Phage capsid scaffolding protein (GPO) serine
peptidase. This family consists of several
bacteriophage capsid scaffolding proteins (GPO) and some
related bacterial sequences. GPO is thought to function
in both the assembly of proheads and the cleavage of
GPN. The family is found to function as a serine
peptidase, with a conserved Asp, His and Ser catalytic
triad, as in subtilisin, and as represented in
MEROPS:S73. The family includes GpO from Enterobacteria
phage P2 which cleaves itself and then becomes the
scaffold protein upon which the bacteriophage prohead is
built - a mechanism quite common amongst phages.
Length = 277
Score = 28.7 bits (64), Expect = 9.5
Identities = 21/111 (18%), Positives = 33/111 (29%), Gaps = 15/111 (13%)
Query: 125 LLAKRKSLFNDKPTEIQELTYIIKEDLNSLNQQIAKLQQVGKHQRDVISSGHQHLLSHSS 184
L + K LF K ++ V +H + + + Q L S +
Sbjct: 175 LFDRVKRLFKKKEASDDA----------RFADVGEAVEAVAEHVQGQLEATEQRL-SEAE 223
Query: 185 SVVLALQSKLASMSTEFKNVLEVRTENLKQAKSRRDQY----SGGGAPSSL 231
V L+ L S E +L Q +GGG + L
Sbjct: 224 KAVSDLEQALNSQGDERDKAFNALKASLSHTDDYAQQARPPATGGGGAAIL 274
>gnl|CDD|204565 pfam10956, DUF2756, Protein of unknown function (DUF2756). Some
members in this family of proteins are annotated yhhA
however currently no function is known. The family
appears to be restricted to Enterobacteriaceae.
Length = 104
Score = 27.3 bits (60), Expect = 9.7
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 259 TALQQQQQQKTMMLYEDQNMSDTALQQQQQQKTM 292
T +Q QQ Q+ ML + + T LQQQ Q +
Sbjct: 41 TQMQTQQIQQKGMLNQQLQ-TQTRLQQQHLQNQL 73
>gnl|CDD|225507 COG2959, HemX, Uncharacterized enzyme of heme biosynthesis
[Coenzyme metabolism].
Length = 391
Score = 29.0 bits (65), Expect = 9.9
Identities = 30/157 (19%), Positives = 48/157 (30%), Gaps = 15/157 (9%)
Query: 206 EVRTENLKQAKSRRDQYSGGGAPSSLPPAAMSGP-------HHQGSVLLADEQCAIDMSD 258
V T + A + G S G Q +VL E A+
Sbjct: 13 AVETPSQPVAPETVSKNGAGLLLSLAALLLALGLGAGGYYFGQQQNVLQTQELQALQQQL 72
Query: 259 TALQ-----QQQQQKTMMLYEDQNMSDTALQQQQQQKTMMLYEDQSEQFIQS--RADTMQ 311
ALQ Q+ + L Q L++Q + L E Q + S
Sbjct: 73 KALQLAQENQKLLAQLESLIAQQQAELDRLERQLETLQKQLSELQKKVATISGSDRKDWL 132
Query: 312 NIES-TIVELGGIFQQLAHMVQEQEEMVERIDANILD 347
E+ +++L G L V +++ DA +
Sbjct: 133 LAEADFLLKLAGRKLVLDQDVTTAVALLKSADARLAA 169
>gnl|CDD|234075 TIGR02968, succ_dehyd_anc, succinate dehydrogenase, hydrophobic
membrane anchor protein. In E. coli and many other
bacteria, two small, hydrophobic, mutually homologous
subunits of succinate dehydrogenase, a TCA cycle enzyme,
are SdhC and SdhD. This family is the SdhD, the
hydrophobic membrane anchor protein. SdhC is
apocytochrome b558, which also plays a role in anchoring
the complex [Energy metabolism, TCA cycle].
Length = 105
Score = 27.1 bits (61), Expect = 10.0
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 435 WLMIKIFAV-LIFFFIFFVVFLAHN 458
WL+ ++ AV L + IF + FL
Sbjct: 8 WLLQRVTAVVLALYTIFLIGFLLAL 32
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
0.320 0.132 0.389
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: 33,012,764
Number of extensions: 3158015
Number of successful extensions: 4637
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4525
Number of HSP's successfully gapped: 122
Length of query: 672
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 569
Effective length of database: 6,369,140
Effective search space: 3624040660
Effective search space used: 3624040660
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 (21.9 bits)
S2: 62 (27.5 bits)