RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15387
(273 letters)
>gnl|CDD|238105 cd00179, SynN, Syntaxin N-terminus domain; syntaxins are nervous
system-specific proteins implicated in the docking of
synaptic vesicles with the presynaptic plasma membrane;
they are a family of receptors for intracellular
transport vesicles; each target membrane may be
identified by a specific member of the syntaxin family;
syntaxins contain a moderately well conserved
amino-terminal domain, called Habc, whose structure is
an antiparallel three-helix bundle; a linker of about 30
amino acids connects this to the carboxy-terminal
region, designated H3 (t_SNARE), of the syntaxin
cytoplasmic domain; the highly conserved H3 region forms
a single, long alpha-helix when it is part of the core
SNARE complex and anchors the protein on the cytoplasmic
surface of cellular membranes; H3 is not included in
defining this domain.
Length = 151
Score = 93.9 bits (234), Expect = 6e-24
Identities = 59/149 (39%), Positives = 88/149 (59%), Gaps = 4/149 (2%)
Query: 38 FMDTVEDSRALIANIQEHVKAMRNLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNS 97
F + VE+ R I I E V+ ++ LHS LL++P D +K EL++ + +KK+AK++
Sbjct: 4 FFEEVEEIRGNIDKISEDVEELQKLHSQLLTAPDADPELKQELESLVQEIKKLAKEIKGK 63
Query: 98 LKKLERSIKKEEDEIEDGHIPASLRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKCEERI 157
LK+LE S ++ E + RIRKTQ S VE +TEFN+ Q Y+E+ +ERI
Sbjct: 64 LKELEESNEQNEALNGS----SVDRIRKTQHSGLSKKFVEVMTEFNKAQRKYRERYKERI 119
Query: 158 QRVVSIARAEISDEKLEELLEQGNYASIF 186
QR + I E +DE+LE++LE GN
Sbjct: 120 QRQLEITGGEATDEELEDMLESGNSEIFT 148
>gnl|CDD|227406 COG5074, COG5074, t-SNARE complex subunit, syntaxin [Intracellular
trafficking and secretion].
Length = 280
Score = 87.6 bits (217), Expect = 3e-20
Identities = 62/238 (26%), Positives = 119/238 (50%), Gaps = 17/238 (7%)
Query: 38 FMDTVEDSRALIANIQEHVKAMRNLHSDLLSSPRQDENMKLE--LDARTETVKKIAKKVS 95
FM+ + ++ ++ + + NLH DLL+ ++++ KL LD + + + +
Sbjct: 23 FMNKILSINKNLSVYEKEINQIDNLHKDLLTEVFEEQSRKLRRSLDNFSSQTTDLQRNLK 82
Query: 96 NSLKKLERSIKKEEDEIEDGHIPASLRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKCEE 155
+K ER D I + ++ Q ++ I ++ +Y+E+ +E
Sbjct: 83 KDIKSAER------DGIHLAN-------KQAQAENVRQKFLKLIQDYRIIDSNYREEEKE 129
Query: 156 RIQRVVSIARAEISDEKLEELLEQGNYASIFNADIV--TETLEARKALEDVQIRHQELLK 213
+ +R IA+ E +++++E + N +F+ ++ EA+ AL +VQ RHQE+ K
Sbjct: 130 QARRQYIIAQPEATEDEVEAAINDVNGQQVFSQALLNANRRGEAKTALAEVQARHQEIKK 189
Query: 214 LEKSIQELRDLFVEMALLVEQQGDIIDSIEHHVMEAGEAVETARVQTKKAIVYQKKAR 271
+EK++ EL LF +M LV +Q + +D I+ +V +A E VE T KA+ + AR
Sbjct: 190 IEKTMAELTQLFNDMEELVIEQQENVDVIDKNVEDAQENVEQGVGHTDKAVKSARAAR 247
>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 = 61.8 bits (151), Expect = 8e-13
Identities = 27/62 (43%), Positives = 39/62 (62%)
Query: 207 RHQELLKLEKSIQELRDLFVEMALLVEQQGDIIDSIEHHVMEAGEAVETARVQTKKAIVY 266
R + L +LE SI EL+ LF++M VE+QG+++D I+ +V VE A + KKA Y
Sbjct: 1 RDEALEELESSIGELKQLFLDMGEEVEEQGELLDRIDDNVDNTQSRVERANKRLKKAARY 60
Query: 267 QK 268
QK
Sbjct: 61 QK 62
>gnl|CDD|214699 smart00503, SynN, Syntaxin N-terminal domain. Three-helix domain
that (in Sso1p) slows the rate of its reaction with the
SNAP-25 homologue Sec9p.
Length = 117
Score = 57.7 bits (140), Expect = 1e-10
Identities = 35/117 (29%), Positives = 62/117 (52%), Gaps = 5/117 (4%)
Query: 38 FMDTVEDSRALIANIQEHVKAMRNLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNS 97
F + VE+ RA I I ++V ++ LH +LL+ P D+ ++ +L+ + +K++AK++
Sbjct: 6 FFEKVEEIRANIQKISQNVAELQKLHEELLTPPDADKELREKLERLIDDIKRLAKEIRAK 65
Query: 98 LKKLERSIKKEEDEIEDGHIPASLRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKCE 154
LK+LE +E+ AS R RK Q E + EF + Q Y+E+ +
Sbjct: 66 LKELE-----KENLENRASGSASDRTRKAQTEKLRKKFKEVMNEFQRLQRKYREREK 117
>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 = 55.1 bits (133), Expect = 6e-10
Identities = 30/102 (29%), Positives = 57/102 (55%), Gaps = 3/102 (2%)
Query: 38 FMDTVEDSRALIANIQEHVKAMRNLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNS 97
F D VE+ R I I+++++ ++ LH +L++P D+ ++ EL+ T+ +K++A+ +
Sbjct: 5 FFDEVEEIREEIQKIRQNLEELQKLHKRILTAPDSDKELREELEELTQEIKQLARAIKKK 64
Query: 98 LKKLERSIKKEEDEIEDGHIPASLRIRKTQQSTTLHLLVEAI 139
LK L++ K E+ GH A RIRK Q + + +
Sbjct: 65 LKSLQQLNKSEQ---GLGHSSAVDRIRKNQLANLSKKFKDVL 103
>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 = 51.0 bits (123), Expect = 6e-09
Identities = 27/66 (40%), Positives = 45/66 (68%)
Query: 198 RKALEDVQIRHQELLKLEKSIQELRDLFVEMALLVEQQGDIIDSIEHHVMEAGEAVETAR 257
++AL + R +EL +LEKSIQEL+ +F++M +E+QG+ +D IE +V +A ++ A
Sbjct: 1 QQALAREEERDEELEQLEKSIQELKQIFLDMGTELEEQGEQLDRIEDNVDDADVNLKKAN 60
Query: 258 VQTKKA 263
+ KKA
Sbjct: 61 KRLKKA 66
>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 = 49.0 bits (118), Expect = 3e-08
Identities = 25/60 (41%), Positives = 39/60 (65%)
Query: 204 VQIRHQELLKLEKSIQELRDLFVEMALLVEQQGDIIDSIEHHVMEAGEAVETARVQTKKA 263
Q R +EL +LE SI EL+ +F+++ VE+QG+++D IE +V A V+ A + KKA
Sbjct: 1 EQERDEELEQLEASIGELKQIFLDLGTEVEEQGELLDRIEDNVDNADVNVKRANKRLKKA 60
>gnl|CDD|227635 COG5325, COG5325, t-SNARE complex subunit, syntaxin [Intracellular
trafficking and secretion].
Length = 283
Score = 44.8 bits (106), Expect = 2e-05
Identities = 38/198 (19%), Positives = 90/198 (45%), Gaps = 22/198 (11%)
Query: 82 ARTETVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPASLRIRKTQQSTTLHLLVEAI-T 140
+ + + +++KKV+ L++ E+ +K + Q S L+ + T
Sbjct: 74 EKEDEIDELSKKVNQDLQRCEKILKTKYKN--------------LQSSFLQSKLLRDLNT 119
Query: 141 EFNQEQLDYKEKCEERIQRVVSIARAEISDEK---LEELLEQGNYASIFNADIVTETLEA 197
E + Q ++ + R +V+ + LEE ++ + +S+ + + + +
Sbjct: 120 ECMEGQRIQQKSAQFRKYQVLQAKFLRNKNNDQHPLEEEEDEESLSSLGSQQTLQQQGLS 179
Query: 198 RKALEDVQIRHQELL----KLEKSIQELRDLFVEMALLVEQQGDIIDSIEHHVMEAGEAV 253
+ LE QI E L + I EL ++F ++ LV +QG+++D I+ ++ + +
Sbjct: 180 NEELEYQQILITERDEEIKNLARGIYELNEIFRDLGSLVGEQGELVDRIDFNIENTSDNL 239
Query: 254 ETARVQTKKAIVYQKKAR 271
+ A + +KA +Q++ +
Sbjct: 240 KNANKELEKAPAHQRRTK 257
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal 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. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 36.2 bits (84), Expect = 0.019
Identities = 42/233 (18%), Positives = 87/233 (37%), Gaps = 17/233 (7%)
Query: 49 IANIQEHVKAMRNLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNSLKKLERSIKKE 108
+ I+ + + SD + E +L+ E +K+ +++ L LE+ I+
Sbjct: 697 LRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENV 756
Query: 109 EDEIEDGHIPASLRIRKTQQSTTLHLLVEAIT--------EFNQEQLDYKEKCEERIQRV 160
+ E+++ L R + LH L EA+ E K EE + R+
Sbjct: 757 KSELKE------LEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRI 810
Query: 161 VSIARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALEDVQIRHQELLKLEKSIQE 220
+ R L ++ I L+ + + +I K E+ +E
Sbjct: 811 EARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEI-ENLNGKKEELEEE 869
Query: 221 LRDLFVEMALLVEQQGDIIDSIEHHVMEAGEAVETARVQTKKAIVYQKKARMS 273
L +L + L + GD+ + + E +++ +A + +K+ R+S
Sbjct: 870 LEELEAALRDLESRLGDLKKERDELEAQLRELER--KIEELEAQIEKKRKRLS 920
Score = 30.4 bits (69), Expect = 1.2
Identities = 48/181 (26%), Positives = 76/181 (41%), Gaps = 21/181 (11%)
Query: 86 TVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPASLRIRKTQQSTTLHLLVEAITEFNQE 145
VK+ ++ + LERSI ++E E+ED A R+ K + + L+ I E +E
Sbjct: 291 RVKEKIGELEAEIASLERSIAEKERELED----AEERLAKLEAE--IDKLLAEIEELERE 344
Query: 146 QLDYKEKCEERIQRVVSIARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALEDVQ 205
EER +R E+LE+L + A+ E + R+ LE ++
Sbjct: 345 IE------EERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLK 398
Query: 206 IRHQELLKLEKSIQELRDLFVEMALLVEQQGDI---IDSIEHHVMEAGEAVETARVQTKK 262
EL +EL L E+ L E+ D+ I IE + E E E ++ KK
Sbjct: 399 REINEL------KRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKK 452
Query: 263 A 263
Sbjct: 453 Q 453
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 35.4 bits (82), Expect = 0.029
Identities = 27/101 (26%), Positives = 55/101 (54%), Gaps = 1/101 (0%)
Query: 79 ELDARTETVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPASLRIRKTQQSTTLHLLVEA 138
E++A+ E +KK KK+ +++LE I+K+E+E+E + K L EA
Sbjct: 92 EIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSNLSEA 151
Query: 139 ITEFNQEQLDYKEKCEERIQRVVSIARAEISDEKLEELLEQ 179
+ N ++ ++KEK + ++ V+ A + +S E+L+ ++
Sbjct: 152 LKGLNYKK-NFKEKLLKELKSVILNASSLLSLEELKAKIKT 191
>gnl|CDD|193443 pfam12970, DUF3858, Domain of Unknown Function with PDB structure
(DUF3858). This family is based on the third domain of
the PDB structure 3KD4(residues 410-525). It is
structurally similar to part of neuropilin-2 (Z=4.6,
rmsd 3.6A for 83 CA, 7% seq id). This domain and the
second domain appears to be part of peptide-n-glycanase
(1x3w, 2g9f).
Length = 116
Score = 33.6 bits (77), Expect = 0.030
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 10/55 (18%)
Query: 73 DENMKLELDARTETVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPASLRIRKTQ 127
E MK + KK+SN++ KL ++KKE D+IE + SL+++K
Sbjct: 46 PEGMKP-------VTPPMEKKISNAVGKLTITVKKEGDKIE---VVRSLKLKKQL 90
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 34.7 bits (80), Expect = 0.060
Identities = 41/234 (17%), Positives = 106/234 (45%), Gaps = 13/234 (5%)
Query: 42 VEDSRALIANIQEHVKAMRNLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNSLKKL 101
+ L+ ++ ++ + +L E +L +R E +++ +++ L++L
Sbjct: 697 LRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEEL 756
Query: 102 ERSIKKEEDEIEDG-HIPASLRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKCEERIQRV 160
+ +++ E+E+E A L+ + L E + E +E + + + + + +
Sbjct: 757 QERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALEREL 816
Query: 161 VSI-ARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALEDVQIRHQELL-KLEKSI 218
S+ R E ++++EEL E+ ++ + E + LE+++ +EL +LE+
Sbjct: 817 ESLEQRRERLEQEIEELEEE-------IEELEEKLDELEEELEELEKELEELKEELEELE 869
Query: 219 QELRDLFVEMALLVEQQGDI---IDSIEHHVMEAGEAVETARVQTKKAIVYQKK 269
E +L E+ L E++ ++ + +E + E E +E R + ++ ++
Sbjct: 870 AEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLER 923
Score = 34.3 bits (79), Expect = 0.065
Identities = 35/241 (14%), Positives = 95/241 (39%), Gaps = 12/241 (4%)
Query: 23 QCLQLTITYSEYHDCFMDTVEDSRALIANIQEHVKAMRNLHSDLLSSPRQDENMKLELDA 82
+ L+L + ++ + +E+ ++ ++E ++ ++ + + ++ EL
Sbjct: 223 RELELALLLAKLKE-LRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELRE 281
Query: 83 RTETVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPASLRIRKTQQSTTLHLLVEAITEF 142
E +++ ++ +++LE I + +E+ L + L L E I
Sbjct: 282 ELEELQEELLELKEEIEELEGEISLLRERLEE------LENELEELEERLEELKEKIEAL 335
Query: 143 NQEQLDYKEKCEERIQRVVSIARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALE 202
+E + + EE Q + + A+ E+ L + + E E L
Sbjct: 336 KEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELF--EALREELAELEAELA 393
Query: 203 DVQIRHQELLKLEKSIQELRDLFVEMALLVEQQGDIIDSIEHHVMEAGEAVETARVQTKK 262
+++ EL +L++ I+ L + ++ +E + + +E + E +E + ++
Sbjct: 394 EIR---NELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELNEELEE 450
Query: 263 A 263
Sbjct: 451 L 451
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 33.7 bits (78), Expect = 0.10
Identities = 31/106 (29%), Positives = 51/106 (48%), Gaps = 21/106 (19%)
Query: 140 TEFNQEQLDYKEKCEERIQRVVSIAR---AEISD--EKLEELLEQGNYASIFNADIVTET 194
EF+ +L+ E ER+ + S+AR I D E L+++ E+ A + N++ E
Sbjct: 292 LEFDPNRLEEVE---ERLFALKSLARKYGVTIEDLLEYLDKIKEE--LAQLDNSEESLEA 346
Query: 195 LEAR---------KALEDV-QIRHQELLKLEKSI-QELRDLFVEMA 229
LE +A E + IR + +LEK + EL+ L +E A
Sbjct: 347 LEKEVKKLKAELLEAAEALSAIRKKAAKELEKEVTAELKALAMEKA 392
>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 = 33.9 bits (78), Expect = 0.11
Identities = 38/172 (22%), Positives = 71/172 (41%), Gaps = 21/172 (12%)
Query: 71 RQDENMKLELDARTETVKKIAKK-------VSNSLKKLERSIKKEEDEIEDGHIPASLRI 123
+ E ++ LDA T + + +K + L++ + I + I
Sbjct: 359 SELEEVEARLDALTGKHQDVQRKYERLKQKIKEQLERDLEKNNERLAAIREEKDRQKAAI 418
Query: 124 RK---TQQSTTLHLLVEAITEFNQEQLDYKEKCEERIQRVVS-------IARAEISDEKL 173
+ +S L EFN+E+ + + + QR+ S + + EI+DE L
Sbjct: 419 EEDLQALESQLRQQLEAGKLEFNEEEYELELRLGRLKQRLDSATATPEELEQLEINDEAL 478
Query: 174 EELLEQGNYASIFNADIVTETLEARK----ALEDVQIRHQELLKLEKSIQEL 221
E+ E+ A + +E + RK ALE +Q + LL+L +++ EL
Sbjct: 479 EKAQEEQEQAEANVEQLQSELRQLRKRRDEALEALQRAERRLLQLRQALDEL 530
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 33.1 bits (76), Expect = 0.16
Identities = 42/205 (20%), Positives = 81/205 (39%), Gaps = 33/205 (16%)
Query: 52 IQEHVKAMRNLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNSLKKLERSIKKEEDE 111
E V+ + + +++ + N+ ++++ + + K+ + K+E +K
Sbjct: 222 YDELVEEAKTIKAEIEELTDELLNLVMDIEDPSAALNKLNTAAAKIKSKIE-QFQKVIKM 280
Query: 112 IEDGHI-PASLRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKCEERIQRVVSIARAEISD 170
E G + P TQQ + + I + +E EK + I + EI D
Sbjct: 281 YEKGGVCPTC-----TQQISEGPDRITKIKDKLKELQHSLEKLDTAIDEL-----EEIMD 330
Query: 171 EKLE---ELLEQGNYASIFNADIVTETLEARKALEDVQIRHQELLKLEKSIQELRDLFV- 226
E E +LLE N S ++T +A+K + +I+EL+ FV
Sbjct: 331 EFNEQSKKLLELKNKISTNKQSLITLVDKAKKV--------------KAAIEELQAEFVD 376
Query: 227 ---EMALLVEQQGDIIDSIEHHVME 248
E+A L ++ I+ + V E
Sbjct: 377 NAEELAKLQDELDKIVKTKSELVKE 401
>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 = 32.3 bits (74), Expect = 0.29
Identities = 32/220 (14%), Positives = 81/220 (36%), Gaps = 5/220 (2%)
Query: 38 FMDTVEDSRALIANIQEHVKAMRNLHSDLLS---SPRQDENMKLELDARTETVKKIAKKV 94
+ L Q + + NL L + E+ EL +++ +++
Sbjct: 290 LYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEEL 349
Query: 95 SNSLKKLERSIKKEEDEIEDGH-IPASLRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKC 153
L+ LE +++ E E+E+ L + + + L I +++ E
Sbjct: 350 KEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIAS-LNNEIERLEAR 408
Query: 154 EERIQRVVSIARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALEDVQIRHQELLK 213
ER++ + EI + + + ++ E E ++ LE ++ +EL +
Sbjct: 409 LERLEDRRERLQQEIEELLKKLEEAELKELQAELEELEEELEELQEELERLEEALEELRE 468
Query: 214 LEKSIQELRDLFVEMALLVEQQGDIIDSIEHHVMEAGEAV 253
+ ++ D ++ + D ++ ++ ++ E V
Sbjct: 469 ELEEAEQALDAAERELAQLQARLDSLERLQENLEGFSEGV 508
Score = 31.6 bits (72), Expect = 0.49
Identities = 41/222 (18%), Positives = 87/222 (39%), Gaps = 12/222 (5%)
Query: 41 TVEDSRALIANIQEHVKAMRNLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNSLKK 100
VE IA + + + + +L + E E +A E ++ +++ LK
Sbjct: 741 EVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKA 800
Query: 101 LERSIKKEEDEIEDGHIPA-SLRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKCEERIQR 159
L ++ + E+ + A +LR R + + + ++ E+ E I+
Sbjct: 801 LREALDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQ----IEELSEDIES 856
Query: 160 V-VSIARAEISDEKLEELLEQ-GNYASIFNADIVTETLEARKALEDVQIRHQELLKLEKS 217
+ I E E+LE LE N + + E + E+++ + +L +
Sbjct: 857 LAAEIEELEELIEELESELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRE 916
Query: 218 IQELRDLFVEMALLVEQQGDIIDSI-----EHHVMEAGEAVE 254
++ELR+ ++ L +E ID++ E + + EA
Sbjct: 917 LEELREKLAQLELRLEGLEVRIDNLQERLSEEYSLTLEEAEA 958
>gnl|CDD|239472 cd03377, TPP_PFOR_PNO, Thiamine pyrophosphate (TPP family),
PFOR_PNO subfamily, TPP-binding module; composed of
proteins similar to the single subunit pyruvate
ferredoxin oxidoreductase (PFOR) of Desulfovibrio
Africanus, present in bacteria and amitochondriate
eukaryotes. This subfamily also includes proteins
characterized as pyruvate NADP+ oxidoreductase (PNO).
These enzymes are dependent on TPP and a divalent metal
cation as cofactors. PFOR and PNO catalyze the oxidative
decarboxylation of pyruvate to form acetyl-CoA, a
crucial step in many metabolic pathways. Archaea,
anaerobic bacteria and eukaryotes that lack mitochondria
(and therefore pyruvate dehydrogenase) use PFOR to
oxidatively decarboxylate pyruvate, with ferredoxin or
flavodoxin as the electron acceptor. The PFOR from
cyanobacterium Anabaena (NifJ) is required for the
transfer of electrons from pyruvate to flavodoxin, which
reduces nitrogenase. The facultative anaerobic
mitochondrion of the photosynthetic protist Euglena
gracilis oxidizes pyruvate with PNO.
Length = 365
Score = 30.6 bits (70), Expect = 0.72
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 155 ERIQRVVSIARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALEDVQIRHQELLKL 214
ER + +V +I DE+L+ LL A + D + E+ E L+ + E +L
Sbjct: 85 ERARELVQKLIEKIGDEELKTLLN----AWLATEDDIEESRERVAKLK--PLLAAEKDEL 138
Query: 215 EKSIQELRDLFVE 227
K + L D V+
Sbjct: 139 AKELLSLADYLVK 151
>gnl|CDD|211958 TIGR04235, seadorna_VP4, seadornavirus VP4 protein. This protein
family occurs in the seadornavirus virus group, with
designation VP4 in Banna virus, Kadipiro virus, and Liao
ning virus. Although this family has been suggested to
resemble methyltransferases, members show apparent
N-terminal sequence similarity to the outer capsid
protein VP5 of the orbivirus group, such as bluetongue
virus, which also belong to the Reoviridae.
Length = 618
Score = 31.0 bits (70), Expect = 0.81
Identities = 34/130 (26%), Positives = 57/130 (43%), Gaps = 16/130 (12%)
Query: 46 RALIANIQEHVKAMR--NLHSDLLSSPRQDEN----MKLELDARTETVKKIAK---KVSN 96
RA+IAN +EH R + D++ S +Q+ +K + A V + K +
Sbjct: 27 RAVIANEREHFMKTRIDRIEHDIIKSTKQEMMDRQVLKEDYKALALAVGQEIKFDNATQH 86
Query: 97 SLKKLERSIKKEEDEIEDGHIPASLRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKCEER 156
L +L +I K + E E I + + + V I E NQ+ + EK +
Sbjct: 87 QLNRLGSAIYKADHEREKELTDLLNAINENEIA------VNDIIE-NQKAITAAEKADLI 139
Query: 157 IQRVVSIARA 166
++ V+S ARA
Sbjct: 140 LEIVISTARA 149
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 30.4 bits (69), Expect = 0.93
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 55 HVKAMRNLHSDLLSSPRQDE-NMKLELDARTETVKKIAKKVSNSLKKLERSIKKEEDEIE 113
++ + L + + K E D + ++ KK+ LKKLE ++K+EDE+E
Sbjct: 251 YLDVVPLKAYADLEKLFNEALDEKFERDKIKQLASELEKKLEKELKKLENKLEKQEDELE 310
Query: 114 D 114
+
Sbjct: 311 E 311
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 30.2 bits (69), Expect = 1.1
Identities = 31/110 (28%), Positives = 41/110 (37%), Gaps = 38/110 (34%)
Query: 158 QRVVSIARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALEDVQIRHQELLKLEKS 217
QRV+ IA A KL L+ AD T L DV + ++L L K
Sbjct: 161 QRVM-IAMALALKPKL--LI----------ADEPTTAL-------DVTTQ-AQILDLLKD 199
Query: 218 IQELRDLFVEMALL--------VEQQGDIIDSIEHHVMEAGEAVETARVQ 259
+Q MA+L V + D + VM GE VET +
Sbjct: 200 LQREL----GMAVLFITHDLGVVAELADRV-----VVMYKGEIVETGPTE 240
>gnl|CDD|213225 cd03258, ABC_MetN_methionine_transporter, ATP-binding cassette
domain of methionine transporter. MetN (also known as
YusC) is an ABC-type transporter encoded by metN of the
metNPQ operon in Bacillus subtilis that is involved in
methionine transport. Other members of this system
include the MetP permease and the MetQ substrate binding
protein. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 233
Score = 29.9 bits (68), Expect = 1.1
Identities = 30/103 (29%), Positives = 43/103 (41%), Gaps = 26/103 (25%)
Query: 158 QRVVSIARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALEDVQIRHQELLKLEKS 217
QRV IARA ++ K+ LL D EA AL D + +L L +
Sbjct: 147 QRV-GIARALANNPKV--LL----------CD------EATSAL-DPETTQS-ILALLRD 185
Query: 218 IQELRDLFVEMALLVEQQGDIIDSIEHH--VMEAGEAVETARV 258
I L + +L+ + +++ I VME GE VE V
Sbjct: 186 INRELGLTI---VLITHEMEVVKRICDRVAVMEKGEVVEEGTV 225
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 30.3 bits (68), Expect = 1.4
Identities = 33/236 (13%), Positives = 85/236 (36%), Gaps = 13/236 (5%)
Query: 39 MDTVEDSRALIANIQEHVKAMRNLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNSL 98
+ V ++ + L + + ++ L+L+ R ++ K+ L
Sbjct: 268 LAQVLKENKEEEKEKKLQEEELKLLAKEE---EELKSELLKLERRKVDDEEKLKESEKEL 324
Query: 99 KKLERSIKKEEDEI-EDGHIPASLRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKCEERI 157
KKLE+ +KKE++EI E L I++ + E E ++ + E+ EE +
Sbjct: 325 KKLEKELKKEKEEIEELEKELKELEIKREAE--------EEEEEQLEKLQEKLEQLEEEL 376
Query: 158 QRVVSIARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALEDVQIRHQELLKLEKS 217
+ +S + E+ + + + + + ++ +E LK+ +
Sbjct: 377 LAKKKLESERLS-SAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEE 435
Query: 218 IQELRDLFVEMALLVEQQGDIIDSIEHHVMEAGEAVETARVQTKKAIVYQKKARMS 273
++E + +++ + + E +TK + ++ +
Sbjct: 436 LEESLETKQGKLTEEKEELEKQALKLLKDKLELKKSEDLLKETKLVKLLEQLELLL 491
>gnl|CDD|223047 PHA03332, PHA03332, membrane glycoprotein; Provisional.
Length = 1328
Score = 29.9 bits (67), Expect = 1.5
Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 2/86 (2%)
Query: 104 SIKKEEDEIEDGHIPASLRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKCEERIQRVVSI 163
I E EI+D +P L + K S + + + + DY+ + + +V++
Sbjct: 1176 QIVSMEGEIQDLKLP-LLTLVKINTSAHMENITGDLDAMKKTIEDYRAEMTQFSAQVMAK 1234
Query: 164 ARAEISDEKLEELLEQG-NYASIFNA 188
R E ++ +I
Sbjct: 1235 LRRTGFGEWIKYFTGPAIGIYAILGV 1260
>gnl|CDD|224494 COG1578, COG1578, Uncharacterized conserved protein [Function
unknown].
Length = 285
Score = 29.3 bits (66), Expect = 2.1
Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 2/56 (3%)
Query: 130 TTLHLLVEAITEFNQEQLDYKEKCEERIQRVVSIARAEISDEKLEELLEQGNYASI 185
T +H V I +YK + E +V+ R I E E L+ +I
Sbjct: 55 TLIHREVYKILGNEDPYKEYKRRANEIALKVLPKVRENI--EDTPEDLKTAVKLAI 108
>gnl|CDD|217334 pfam03041, Baculo_LEF-2, lef-2. The lef-2 gene (for late
expression factor 2) from baculovirus is required for
expression of late genes. This gene has been shown to be
specifically required for expression from the vp39 and
polh promoters. LEF-1 is a DNA primase and there is some
evidence to suggest that LEF-2 may bind to both DNA and
LEF-1.
Length = 164
Score = 28.5 bits (64), Expect = 2.3
Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 10/71 (14%)
Query: 11 RIKALRVSCVMDQCLQLTITYSEYHD-------CFMDTVEDSRALIANIQEHVK---AMR 60
R+ LR+ ++ + S CF D +++I +++ + +
Sbjct: 46 RVSGLRLYNLLKNPPTFEESPSVNFSKKSKRNVCFKDCSGGRKSVIDKLRKLLNPPPCIT 105
Query: 61 NLHSDLLSSPR 71
+DL PR
Sbjct: 106 KALNDLCVRPR 116
>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
This family consists of the N-terminal region of the
prokaryotic fibronectin-binding protein. Fibronectin
binding is considered to be an important virulence
factor in streptococcal infections. Fibronectin is a
dimeric glycoprotein that is present in a soluble form
in plasma and extracellular fluids; it is also present
in a fibrillar form on cell surfaces. Both the soluble
and cellular forms of fibronectin may be incorporated
into the extracellular tissue matrix. While fibronectin
has critical roles in eukaryotic cellular processes,
such as adhesion, migration and differentiation, it is
also a substrate for the attachment of bacteria. The
binding of pathogenic Streptococcus pyogenes and
Staphylococcus aureus to epithelial cells via
fibronectin facilitates their internalisation and
systemic spread within the host.
Length = 447
Score = 29.1 bits (66), Expect = 2.3
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 77 KLELDARTETVKKIAKKVSNSLKKLERSIKKEEDEIED 114
K E D + + K+V N L+KLE+ ++K E E+E+
Sbjct: 284 KAERDRVKQKRSDLEKRVENELEKLEKKLEKLEKELEE 321
>gnl|CDD|182854 PRK10941, PRK10941, hypothetical protein; Provisional.
Length = 269
Score = 28.8 bits (65), Expect = 2.6
Identities = 13/30 (43%), Positives = 21/30 (70%), Gaps = 5/30 (16%)
Query: 154 EERIQRVVSIARAEIS-----DEKLEELLE 178
+ ++R+VS+AR EIS DE+LE+L+
Sbjct: 35 YDELERLVSLAREEISQLLPQDEQLEKLIA 64
>gnl|CDD|233879 TIGR02468, sucrsPsyn_pln, sucrose phosphate synthase/possible
sucrose phosphate phosphatase, plant. Members of this
family are sucrose-phosphate synthases of plants. This
enzyme is known to exist in multigene families in
several species of both monocots and dicots. The
N-terminal domain is the glucosyltransferase domain.
Members of this family also have a variable linker
region and a C-terminal domain that resembles sucrose
phosphate phosphatase (SPP) (EC 3.1.3.24) (see
TIGR01485), the next and final enzyme of sucrose
biosynthesis. The SPP-like domain likely serves a
binding and not a catalytic function, as the reported
SPP is always encoded by a distinct protein.
Length = 1050
Score = 29.4 bits (66), Expect = 2.6
Identities = 23/107 (21%), Positives = 33/107 (30%), Gaps = 14/107 (13%)
Query: 61 NLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPAS 120
NL D + + V KI V + K + S K + G PA
Sbjct: 707 NLSVDGDKESNNGSSNVEGSGPPADRVAKIENAVRSWSKSPKGSSAKAQQGSGAGKYPA- 765
Query: 121 LRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKCEERIQRVVSIARAE 167
LR RK L V A+ + + I+ + R E
Sbjct: 766 LRRRK-------RLFVIAV------DCYDDKDLLQIIKNIFEAVRKE 799
>gnl|CDD|217617 pfam03567, Sulfotransfer_2, Sulfotransferase family. This family
includes a variety of sulfotransferase enzymes.
Chondroitin 6-sulfotransferase catalyzes the transfer of
sulfate to position 6 of the N-acetylgalactosamine
residue of chondroitin. This family also includes
Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan
sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS)
is a co-receptor for a number of growth factors,
morphogens, and adhesion proteins. HS biosynthetic
modifications may determine the strength and outcome of
HS-ligand interactions. Mice that lack HS2ST undergo
developmental failure only after midgestation,the most
dramatic effect being the complete failure of kidney
development. Heparan sulphate 6- O -sulfotransferase
(HS6ST) catalyzes the transfer of sulphate from
adenosine 3'-phosphate, 5'-phosphosulphate to the 6th
position of the N -sulphoglucosamine residue in heparan
sulphate.
Length = 238
Score = 28.5 bits (64), Expect = 2.9
Identities = 23/149 (15%), Positives = 49/149 (32%), Gaps = 20/149 (13%)
Query: 6 WYYHQRIKALRVS---CVMDQCLQLT--ITYSEYHDCFMDTVEDSRALIANIQEHVKAMR 60
Y ++ + A S C + +++ E F++ + + H
Sbjct: 91 AYRNKCVGANYGSDMRCKGRKPTDDGSGVSFEE----FVECLLNLAPERTYFDRHWAPQC 146
Query: 61 NLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPAS 120
+L L +K +L + ET+++ A + L+ L R ++ IP
Sbjct: 147 DLCHPCL--------IKYDLVGKYETLEEDASAI---LRLLGRLRRQGVPLFGLEEIPRD 195
Query: 121 LRIRKTQQSTTLHLLVEAITEFNQEQLDY 149
L + +T L E + +
Sbjct: 196 LETAHSTHRSTKRLEAEYFVRIDPKLRRR 224
>gnl|CDD|235616 PRK05813, PRK05813, single-stranded DNA-binding protein;
Provisional.
Length = 219
Score = 28.1 bits (63), Expect = 4.1
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 84 TETVKKIAKKVSNSLKKLERSIKKEEDEIED 114
E V K+A +VS S K+E+ K+E + E
Sbjct: 189 GEVVTKVAYEVSIS--KMEKVEKEEANNKEK 217
>gnl|CDD|238777 cd01519, RHOD_HSP67B2, Member of the Rhodanese Homology Domain
superfamily. This CD includes the heat shock protein
67B2 of Drosophila melanogaster and other similar
proteins, many of which are uncharacterized.
Length = 106
Score = 27.2 bits (61), Expect = 4.1
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 107 KEEDEIEDGHIPASLRIRKTQQSTTLHL 134
+E +E++ G IP ++ I + L L
Sbjct: 22 REPEELKTGKIPGAINIPLSSLPDALAL 49
>gnl|CDD|218806 pfam05911, DUF869, Plant protein of unknown function (DUF869).
This family consists of a number of sequences found in
Arabidopsis thaliana, Oryza sativa and Lycopersicon
esculentum (Tomato). The function of this family is
unknown.
Length = 767
Score = 28.8 bits (64), Expect = 4.3
Identities = 22/112 (19%), Positives = 40/112 (35%), Gaps = 3/112 (2%)
Query: 19 CVMDQCLQLTITYSEYHDCFMDTVEDSRALIANIQEHVKAMRNLHSDLLSSPRQDENMKL 78
+++ L +D +QE K + L S+L +S + +
Sbjct: 591 STLEELETLKSEKENLDGELSKCKDDLEESKNKLQETEKKLEELKSELDASQESNSLAET 650
Query: 79 ELDARTETVKKI---AKKVSNSLKKLERSIKKEEDEIEDGHIPASLRIRKTQ 127
+L E+ + + AK + K L+ I EDE+E I K +
Sbjct: 651 QLKCMVESYESLELRAKDLEAEHKSLQEKISSLEDELEKERQNHQELIAKCR 702
>gnl|CDD|224465 COG1548, COG1548, Predicted transcriptional regulator/sugar kinase
[Transcription / Carbohydrate transport and metabolism].
Length = 330
Score = 28.2 bits (63), Expect = 4.4
Identities = 14/54 (25%), Positives = 23/54 (42%)
Query: 151 EKCEERIQRVVSIARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALEDV 204
E+C R+ R V E+ +E++ +L E+ A + E R L V
Sbjct: 229 EECMRRLARTVCADLEELGEEEVIDLAEKAYNALLELLAENIEEKAKRYGLNTV 282
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 28.6 bits (64), Expect = 4.6
Identities = 24/163 (14%), Positives = 62/163 (38%), Gaps = 15/163 (9%)
Query: 66 LLSSPRQDENMKLELDARTETVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPASLR-IR 124
+L+S ++ E + E + K+V +++ + K +ED I ++ I
Sbjct: 1303 ILNSTKKAEEFSNDAKKELEKTDNLIKQVEAKIEQAKEHKNKIYGSLEDKQIDDEIKKIE 1362
Query: 125 KTQQSTTLHLLVEAITEFNQEQLDYKEKCEERIQRVV-SIARAEISDEKLEELLEQGNYA 183
+ ++ + + I ++ KEKC+ ++ + + ++ + + +
Sbjct: 1363 QIKEEIS--NKRKEINKYLSNIKSNKEKCDLHVRNASRGKDKIDFLNKHEA---IEPSNS 1417
Query: 184 SIFNADIVTETL--------EARKALEDVQIRHQELLKLEKSI 218
N +T+ + EA + + ++K EK I
Sbjct: 1418 KEVNIIKITDNINKCKQYSNEAMETENKADENNDSIIKYEKEI 1460
>gnl|CDD|234309 TIGR03683, A-tRNA_syn_arch, alanyl-tRNA synthetase. This family of
alanyl-tRNA synthetases is limited to the archaea, and
is a subset of those sequences identified by the model
pfam07973 covering the second additional domain (SAD) of
alanyl and threonyl tRNA synthetases.
Length = 902
Score = 28.4 bits (64), Expect = 5.6
Identities = 30/142 (21%), Positives = 54/142 (38%), Gaps = 42/142 (29%)
Query: 88 KKIAKKVSNSLKKLERSIKKEED-------------EIEDGHIP--------ASLRIRKT 126
KK+A K+ +++LE+ I E + DG +P A L IR+T
Sbjct: 305 KKVADKIGIDVEELEKIIAPVERIYAIADHTRCLAFMLGDGIVPSNVKEGYLARLVIRRT 364
Query: 127 QQ-------STTLHLLVEAITEFNQEQLDYKEKCEERIQRVVSIARAEISDEKLEELLEQ 179
+ L LVE E ++ ++ ++ I ++ ++ +EK E LE+
Sbjct: 365 LRLMRELGLDIPLSDLVEMQLEELKKIYPELKENKDYILDIL-----DLEEEKYRETLER 419
Query: 180 G---------NYASIFNADIVT 192
G I D++
Sbjct: 420 GRRIVERLLKTKKEIPLDDLIE 441
>gnl|CDD|215018 smart01087, COG6, Conserved oligomeric complex COG6. COG6 is a
component of the conserved oligomeric golgi complex,
which is composed of eight different subunits and is
required for normal golgi morphology and localisation.
Length = 598
Score = 28.1 bits (63), Expect = 5.6
Identities = 13/66 (19%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 48 LIANIQEHVKAMRNLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNSLK-KLERSIK 106
IAN +E ++++ ++ +EN++ D + + +I + + L+ ++E+ ++
Sbjct: 252 TIANEKEFLESL----FKKVTKQGIEENLQDLEDLDNKLLDRILEGLCRPLRIRIEQVLQ 307
Query: 107 KEEDEI 112
EE I
Sbjct: 308 SEEGAI 313
>gnl|CDD|226234 COG3711, BglG, Transcriptional antiterminator [Transcription].
Length = 491
Score = 28.2 bits (63), Expect = 5.8
Identities = 20/89 (22%), Positives = 42/89 (47%), Gaps = 4/89 (4%)
Query: 67 LSSPRQDENMKLELDARTE-TVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPASLRIRK 125
+ R+++ + L L T+K++A+++ S + + IKK + +E+G IP I++
Sbjct: 1 MLLTRREQLLLLLLLKNPLLTIKELAEQLGVSRRTIRYDIKKINESLEEGGIPI---IKR 57
Query: 126 TQQSTTLHLLVEAITEFNQEQLDYKEKCE 154
L A+ ++L +K E
Sbjct: 58 KGGGYILEEDERALELEELQELTSYDKDE 86
>gnl|CDD|225019 COG2108, COG2108, Uncharacterized conserved protein related to
pyruvate formate-lyase activating enzyme [General
function prediction only].
Length = 353
Score = 28.1 bits (63), Expect = 5.8
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 136 VEAITEFNQEQLDYKEKCEERIQRVVSIARAEISDEKLEELLEQGNYASIFNADIVTETL 195
+ AI + L++ + +E ++I E S+ E LLE+G S + V +L
Sbjct: 171 IPAIPGEEEAILEFAKALDENGLDFLNINELEFSENNYENLLERGYKISDDGSSAVAGSL 230
Query: 196 E-ARKALEDV 204
E A K L+
Sbjct: 231 EAALKVLKWA 240
>gnl|CDD|106256 PRK13296, PRK13296, tRNA CCA-pyrophosphorylase; Provisional.
Length = 360
Score = 28.0 bits (62), Expect = 6.1
Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 8/88 (9%)
Query: 160 VVSIARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALEDVQIRHQELLKLEKSIQ 219
++ I + ++ D + E LL +Y ++ ++ K LED I +E+ +L K+
Sbjct: 239 LLKIPQQQLDDIRKELLLTNKHY------KLLKASIAISKILEDRSITAEEIFQLIKNAN 292
Query: 220 ELRD--LFVEMALLVEQQGDIIDSIEHH 245
+RD LF E L ++ I D+I H
Sbjct: 293 IIRDKNLFAESLNLYKKYLKICDTITPH 320
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 28.0 bits (63), Expect = 6.4
Identities = 22/120 (18%), Positives = 51/120 (42%), Gaps = 12/120 (10%)
Query: 151 EKCEERIQRVVSIARAEISDEKLEELLEQGNYASIFNADIVTETLEARKALE-DVQIRHQ 209
EE +R++ A+ E K E LLE E + R LE +++ R
Sbjct: 28 GSAEELAKRIIEEAKKEAETLKKEALLEAKE-----------EVHKLRAELERELKERRN 76
Query: 210 ELLKLEKSIQELRDLFVEMALLVEQQGDIIDSIEHHVMEAGEAVETARVQTKKAIVYQKK 269
EL +LE+ + + + ++++ + ++ E + + ++ + ++ I Q++
Sbjct: 77 ELQRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQRE 136
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 27.8 bits (62), Expect = 6.7
Identities = 31/185 (16%), Positives = 65/185 (35%), Gaps = 14/185 (7%)
Query: 81 DARTETVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPASLRIRKTQQS---TTLHLLV- 136
ET + KK+ + L + E + + + ++ Q+S LLV
Sbjct: 80 AQLIETADDL-KKLRKQIADLNARLNALEVQEREQRRRLAEQLAALQRSGRNPPPALLVS 138
Query: 137 -EAITEFNQEQLDYKEKCEERIQRVVSIA--RAEISDEKLEELLEQGNYASIFNADIVTE 193
E + + Y R +R+ ++ +++ + E EQ A + ++E
Sbjct: 139 PEDAQRSVRLAIYYGALNPARAERIDALKATLKQLAAVRAEIAAEQ---AELTTL--LSE 193
Query: 194 TLEARKALEDVQIRHQELL-KLEKSIQELRDLFVEMALLVEQQGDIIDSIEHHVMEAGEA 252
+ L + ++ L +L + + E+ + + I S E +A EA
Sbjct: 194 QRAQQAKLAQLLEERKKTLAQLNSELSADQKKLEELRANESRLKNEIASAEAAAAKAREA 253
Query: 253 VETAR 257
A
Sbjct: 254 AAAAE 258
>gnl|CDD|143454 cd07136, ALDH_YwdH-P39616, Bacillus subtilis aldehyde dehydrogenase
ywdH-like. Uncharacterized Bacillus subtilis ywdH
aldehyde dehydrogenase (locus P39616) most closely
related to the ALDHs and fatty ALDHs of families 3 and
14, and similar sequences, are included in this CD.
Length = 449
Score = 27.9 bits (63), Expect = 6.9
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 96 NSLKKLERSIKKEEDEIED 114
LKKL+++IKK E+EI +
Sbjct: 24 EQLKKLKQAIKKYENEILE 42
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 28.0 bits (63), Expect = 7.3
Identities = 30/150 (20%), Positives = 61/150 (40%), Gaps = 16/150 (10%)
Query: 43 EDSRALIANIQEHVKAMRNLHSDLLSSPRQDENMKLELDARTETVKKIAKKVSNSLKKL- 101
E++ ++E + A+RNL +++ SP +K+ L E + + + +K L
Sbjct: 718 EEAEKEFELLKEIISAIRNLRAEMNLSPSA--PLKVVLVGSEEL-EDRLEANEDDIKGLA 774
Query: 102 ---ERSIKKEEDEIEDGHIPASLRIRKTQQSTTLHLLVEAITEFNQEQLDYKEKCEERIQ 158
E I + E + A + + + + A +++L+ EK +RI+
Sbjct: 775 NLEELEILSPDPEEPPVEVTAVVGGAELFLPLAGLIDLAAELARLEKELEKLEKEIDRIE 834
Query: 159 ------RVVSIARAEISD---EKLEELLEQ 179
V+ A E+ + EKL E +
Sbjct: 835 KKLSNEGFVAKAPEEVVEKEKEKLAEYQVK 864
>gnl|CDD|223441 COG0364, Zwf, Glucose-6-phosphate 1-dehydrogenase [Carbohydrate
transport and metabolism].
Length = 483
Score = 27.2 bits (61), Expect = 9.5
Identities = 9/36 (25%), Positives = 19/36 (52%)
Query: 149 YKEKCEERIQRVVSIARAEISDEKLEELLEQGNYAS 184
YKE R++ +AR++ S+E+ L+ + +
Sbjct: 32 YKEGLLPEDFRIIGVARSKWSNEEFRALVREAIEFA 67
>gnl|CDD|145973 pfam03114, BAR, BAR domain. BAR domains are dimerisation, lipid
binding and curvature sensing modules found in many
different protein families. A BAR domain with an
additional N-terminal amphipathic helix (an N-BAR) can
drive membrane curvature. These N-BAR domains are found
in amphiphysin, endophilin, BRAP and Nadrin. BAR domains
are also frequently found alongside domains that
determine lipid specificity, like pfam00169 and
pfam00787 domains in beta centaurins and sorting nexins
respectively.
Length = 230
Score = 26.9 bits (60), Expect = 9.7
Identities = 26/147 (17%), Positives = 55/147 (37%), Gaps = 18/147 (12%)
Query: 17 VSCVMDQCLQLTITY-SEYHDCFMDTVEDSRALIANIQEHVKAMRNLHSDLLSSPRQDEN 75
M Q QL F+D + + +IQ+H+K + E
Sbjct: 97 YGEAMKQLAQLLEQLDDRLRSNFLDPLRNLLKEFKDIQKHIKKL--------------ER 142
Query: 76 MKLELDARTETVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPASLRIRKTQQSTTLHLL 135
+L+ DA+ +KK K L K E +++ + + E+ + + +
Sbjct: 143 KRLDYDAKRHRLKKAKSK--KELSKAEEELRQAQQKFEESNEELKEELPNLLALEV-EFV 199
Query: 136 VEAITEFNQEQLDYKEKCEERIQRVVS 162
V + F + QLD+ + + ++++
Sbjct: 200 VNCLQAFVEAQLDFHRQSYQLLEQLQQ 226
>gnl|CDD|237110 PRK12472, PRK12472, hypothetical protein; Provisional.
Length = 508
Score = 27.5 bits (61), Expect = 9.7
Identities = 30/137 (21%), Positives = 55/137 (40%), Gaps = 12/137 (8%)
Query: 72 QDENMKLELDART--ETVKKIAKKVSNSLKKLERSIKKEEDEIEDGHIPASLRIRKTQQS 129
++ + +A+T + A + SL+KLER+ + + E++ +L KT ++
Sbjct: 199 AEDAARAADEAKTAAAAAAREAAPLKASLRKLERAKARADAELK--RADKALAAAKTDEA 256
Query: 130 TTLHLLVEAITEFNQEQLDYKEKCEERIQRVVSIARAEISDEKLEELLEQGNYASIFNAD 189
+A E Q++ + E Q + A AE E A+ A+
Sbjct: 257 -------KARAEERQQKAAQQAA-EAATQLDTAKADAEAKRAAAAATKEAAKAAAAKKAE 308
Query: 190 IVTETLEARKALEDVQI 206
+A+ ALE V I
Sbjct: 309 TAKAATDAKLALEPVSI 325
>gnl|CDD|213356 cd12822, TmCorA-like, Thermotoga maritima CorA-like family. This
family belongs to the MIT superfamily of essential
membrane proteins involved in transporting divalent
cations (uptake or efflux) across membranes. Members of
the Thermotoga maritima CorA_like family are found in
all three kingdoms of life. It is a functionally diverse
family, in addition to the CorA Co2+ transporter from
the hyperthermophilic Thermotoga maritima, it includes
three Saccharomyces cerevisiae members: two plasma
membrane proteins, the Mg2+ transporter Alr1p/Swc3p and
the putative Mg2+ transporter, Alr2p, and the vacuole
membrane protein Mnr2p, a putative Mg2+ transporter.
Thermotoga maritima CorA forms funnel-shaped
homopentamers, the tip of the funnel is formed from two
C-terminal transmembrane (TM) helices from each monomer,
and the large opening of the funnel from the N-terminal
cytoplasmic domains. The GMN signature motif of the MIT
superfamily occurs just after TM1, mutation within this
motif is known to abolish Mg2+ transport by Alr1p.
Natural variants in this signature sequence may be
associated with the transport of different divalent
cations. The functional diversity of the MIT superfamily
may also be due to minor structural differences
regulating gating, substrate selection, and transport.
Length = 289
Score = 27.1 bits (61), Expect = 9.9
Identities = 21/135 (15%), Positives = 50/135 (37%), Gaps = 44/135 (32%)
Query: 132 LHLLVEAITEFNQEQLDYKEKCEERIQRVVSIARAEISDEKLEELLEQGNYASIFNADIV 191
L+ +++AI + LD + E+R+ ++LE+ + + +++
Sbjct: 108 LYAILDAIVDSYFPILD---ELEDRL-------------DELEDEILEEP-----RREVL 146
Query: 192 TETLEARKALEDVQIRHQELLKLEKSIQELRDLFVEMALLVEQQ---------GDIIDSI 242
E R+ ELL+L + + R++ + + D+ D
Sbjct: 147 RELFALRR----------ELLRLRRILSPQREVLNRLLRRENELISEELRPYFRDVYD-- 194
Query: 243 EHHVMEAGEAVETAR 257
H+ E +++ R
Sbjct: 195 --HLERLAELLDSYR 207
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
0.316 0.130 0.346
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,665,464
Number of extensions: 1339759
Number of successful extensions: 2884
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2750
Number of HSP's successfully gapped: 309
Length of query: 273
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 178
Effective length of database: 6,723,972
Effective search space: 1196867016
Effective search space used: 1196867016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.1 bits)