RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12048
(267 letters)
>gnl|CDD|117826 pfam09282, Mago-bind, Mago binding. Members of this family adopt
a structure consisting of a small globular
all-beta-domain, with a three-stranded beta-sheet and a
contiguous beta-hairpin. They bind to Mago
alpha-helices via extensive electrostatic interactions
and at a beta2-beta3 loop via hydrophobic interactions.
Length = 27
Score = 44.9 bits (107), Expect = 5e-07
Identities = 14/24 (58%), Positives = 18/24 (75%)
Query: 4 YIQPSRRPDGTFRKAIRVKAGYVP 27
I ++RPDG+FRK IRV+ GY P
Sbjct: 4 IIPETQRPDGSFRKEIRVRPGYTP 27
>gnl|CDD|221998 pfam13234, rRNA_proc-arch, rRNA-processing arch domain. Mtr4 is
the essential RNA helicase, and is an exosome-activating
cofactor. This arch domain is carried in Mtr4 and Ski2
(the cytosolic homologue of Mtr4). The arch domain is
required for proper 5.8S rRNA processing, and appears to
function independently of canonical helicase activity.
Length = 266
Score = 34.1 bits (79), Expect = 0.056
Identities = 16/48 (33%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 204 NLKKKVREIKTLEQKIESGEI-KNPEKDQL-EKLQRKPDLLSEIMALK 249
+ KK +R+I+ LE ++ S + +P ++L ++ +K +L EI ALK
Sbjct: 213 SFKKLLRKIEVLESRLLSNPLHNSPRLEELYDQYSKKVELEEEIKALK 260
>gnl|CDD|237616 PRK14127, PRK14127, cell division protein GpsB; Provisional.
Length = 109
Score = 32.7 bits (75), Expect = 0.058
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 11/66 (16%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIK 203
EEL++ LK +V E+T QV+ P+ S N+D L KR+
Sbjct: 47 EELQQENARLKAQVDELTKQVSVGASSSSVAT-----TQPSSSATNYDIL------KRLS 95
Query: 204 NLKKKV 209
NL+K V
Sbjct: 96 NLEKHV 101
>gnl|CDD|232901 TIGR00275, TIGR00275, flavoprotein, HI0933 family. The model when
searched with a partial length search brings in proteins
with a dinucleotide-binding motif (Rossman fold) over
the initial 40 residues of the model, including
oxidoreductases and dehydrogenases. Partially
characterized members include an FAD-binding protein
from Bacillus cereus and flavoprotein HI0933 from
Haemophilus influenzae [Unknown function, Enzymes of
unknown specificity].
Length = 400
Score = 33.3 bits (77), Expect = 0.098
Identities = 29/117 (24%), Positives = 52/117 (44%), Gaps = 24/117 (20%)
Query: 130 PPAPSELNF-DNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSEL 188
E++ +LS EELE+R+K L+K + TV+ +P++L + + +L
Sbjct: 253 KGVELEIDLLPDLSEEELEQRLKRLRKSNPKKTVKNILKGLLPKRLAELLLEQLGIDPDL 312
Query: 189 NFDNLSPEELEKRIKNLKK---------------------KVREI--KTLEQKIESG 222
LS +E++K ++ LK ++EI KT+E K+ G
Sbjct: 313 PAAQLSKKEIKKLVQLLKNWPFTISGTRGFKEAEVTAGGVSLKEINPKTMESKLVPG 369
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 33.0 bits (76), Expect = 0.10
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 197 ELEKRIKNLKKKVRE----IKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEIMALK 249
ELE+ IK L+++ E + LE K+E K E+++ + +R D EI LK
Sbjct: 124 ELEQEIKKLEEEKEELEKRVAELEAKLE-AIEKREEEERQIEEKRHAD---EIAFLK 176
Score = 27.6 bits (62), Expect = 5.4
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 31/80 (38%)
Query: 145 ELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIKN 204
ELE+ IK L+++ E+ +V ELE +++
Sbjct: 124 ELEQEIKKLEEEKEELEKRV-------------------------------AELEAKLEA 152
Query: 205 LKKKVREIKTLEQKIESGEI 224
++K+ E + +E+K + EI
Sbjct: 153 IEKREEEERQIEEKRHADEI 172
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 32.7 bits (75), Expect = 0.18
Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 8/99 (8%)
Query: 134 SELNFDNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNL 193
EL EEL+K++K L+K++ E+ + E + LK L
Sbjct: 331 KELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKK------RLTGL 384
Query: 194 SPEELEKRIKNLKKKVREIKTLEQKIES--GEIKNPEKD 230
+PE+LEK ++ L+K EI+ KI + GE+K K+
Sbjct: 385 TPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKE 423
Score = 32.7 bits (75), Expect = 0.22
Identities = 28/123 (22%), Positives = 56/123 (45%), Gaps = 9/123 (7%)
Query: 134 SELNFDNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVS-LKPPAPSELNFDN 192
E+ E LE + L++K+RE+ ++ + +L KV LK +
Sbjct: 238 EEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIK 297
Query: 193 LSP--EELEKRIKNLKKKV----REIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEIM 246
LS EE ++ ++K++ EI +E++I+ E K ++L+K + +L +
Sbjct: 298 LSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKK--KLKELEKRLE 355
Query: 247 ALK 249
L+
Sbjct: 356 ELE 358
Score = 30.0 bits (68), Expect = 1.3
Identities = 28/115 (24%), Positives = 49/115 (42%), Gaps = 14/115 (12%)
Query: 142 SPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKR 201
S EELE+R+K L+ E E+ R+ L+ EEL+K
Sbjct: 586 SVEELEERLKELEPFYNEYLELKDAEKELEREEKELKKLE--------------EELDKA 631
Query: 202 IKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEIMALKLSLHGEE 256
+ L + + ++ L +++E E K E++ E + +L E+ L+ L E
Sbjct: 632 FEELAETEKRLEELRKELEELEKKYSEEEYEELREEYLELSRELAGLRAELEELE 686
Score = 29.6 bits (67), Expect = 2.0
Identities = 32/108 (29%), Positives = 53/108 (49%), Gaps = 19/108 (17%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIK 203
E +E+ IK +K++ E+ R++N S P EL E+LEK +K
Sbjct: 189 ENIEELIKEKEKELEEVL----------REINEISSELPELREEL-------EKLEKEVK 231
Query: 204 NLKKKVREIKTLEQKIES--GEIKNPEKDQLEKLQRKPDLLSEIMALK 249
L++ EI+ LE+++ES G + E+ E +R +L EI L+
Sbjct: 232 ELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELE 279
Score = 28.9 bits (65), Expect = 3.8
Identities = 31/150 (20%), Positives = 60/150 (40%), Gaps = 33/150 (22%)
Query: 140 NLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSEL----------- 188
L+PE+LEK ++ L+K EI +++ +L ++ A EL
Sbjct: 383 GLTPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKAKGKCPVCG 442
Query: 189 ------------NFDNLSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPE-------K 229
+ +EK +K +++K R+++ +++E K E
Sbjct: 443 RELTEEHRKELLEEYTAELKRIEKELKEIEEKERKLRKELRELEKVLKKESELIKLKELA 502
Query: 230 DQLEKLQRKPDLLSEIMALKLSLHGEEGEG 259
+QL++L+ K L + +L EE E
Sbjct: 503 EQLKELEEK---LKKYNLEELEKKAEEYEK 529
Score = 28.1 bits (63), Expect = 5.2
Identities = 20/91 (21%), Positives = 44/91 (48%), Gaps = 7/91 (7%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIK 203
+L + + ++REI +++ E + ++ EL EEL+K++K
Sbjct: 296 IKLSEFYEEYLDELREIEKRLSRLEEEINGIEERIK-------ELEEKEERLEELKKKLK 348
Query: 204 NLKKKVREIKTLEQKIESGEIKNPEKDQLEK 234
L+K++ E++ + E + K E ++L+K
Sbjct: 349 ELEKRLEELEERHELYEEAKAKKEELERLKK 379
Score = 28.1 bits (63), Expect = 5.6
Identities = 21/106 (19%), Positives = 47/106 (44%), Gaps = 15/106 (14%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPE------- 196
EE+ + I + ++ E+ ++ E + ++ EL + S E
Sbjct: 203 EEVLREINEISSELPELREEL----EKLEKEVKELEELKEEIEELEKELESLEGSKRKLE 258
Query: 197 ----ELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRK 238
ELE+RI+ LKK++ E++ ++++ + K E +L + +
Sbjct: 259 EKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEE 304
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 32.8 bits (75), Expect = 0.20
Identities = 32/135 (23%), Positives = 54/135 (40%), Gaps = 16/135 (11%)
Query: 144 EELEKRIKNLKKK---VREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEK 200
+ELEK L K EI V + E+ ++ +V LK +L +E E+
Sbjct: 133 DELEKEADELWKPRGRKPEINVALKELKELEAEIR-EVQLKTRTWKDLVKAL---DEAEE 188
Query: 201 RIKNLKKKVREIKTLEQKIE--------SGEIKNPEKDQLEKLQRKPDLLSEIMALKLSL 252
+ NL+K++R+++ +Q++E E K E+ QL L DL + +
Sbjct: 189 ELANLRKELRQLEKEKQRLERLRRLLPLLAERKALEQ-QLAALGEVIDLPPDAVERYEEA 247
Query: 253 HGEEGEGEGTHAKYT 267
E T
Sbjct: 248 RAELRAARRNLELLT 262
>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 = 32.0 bits (73), Expect = 0.41
Identities = 33/121 (27%), Positives = 58/121 (47%), Gaps = 12/121 (9%)
Query: 134 SELNFDNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNL 193
+LN L E LEK I+ L+++ ++ Q+ + +++ K EL
Sbjct: 819 QKLNRLTLEKEYLEKEIQELQEQRIDLKEQI---KSIEKEIENLNGKKEELEEELEELEA 875
Query: 194 SPEELEKRIKNLKKKVRE----IKTLEQKIESGEIKNPEK-----DQLEKLQRKPDLLSE 244
+ +LE R+ +LKK+ E ++ LE+KIE E + +K + KL+ + LSE
Sbjct: 876 ALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEALEEELSE 935
Query: 245 I 245
I
Sbjct: 936 I 936
Score = 28.1 bits (63), Expect = 6.0
Identities = 21/102 (20%), Positives = 50/102 (49%), Gaps = 1/102 (0%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIK 203
+ELE +++ L++K+ E+ Q+ + +L K+ SE+ EE+ +
Sbjct: 892 DELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEALEEELSEIEDPKGEDEEIPEEEL 951
Query: 204 NLKKKVREIKTLEQKIES-GEIKNPEKDQLEKLQRKPDLLSE 244
+L+ E++ +E++I + + + E++ ++ D L E
Sbjct: 952 SLEDVQAELQRVEEEIRALEPVNMLAIQEYEEVLKRLDELKE 993
>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 = 31.0 bits (71), Expect = 0.57
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 196 EELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSE 244
E LEK+ K L K + + E+++E +Q E+L+R L E
Sbjct: 104 ENLEKKEKELSNKEKNLDEKEEELE-----ELIAEQREELERISGLTQE 147
>gnl|CDD|227514 COG5187, RPN7, 26S proteasome regulatory complex component,
contains PCI domain [Posttranslational modification,
protein turnover, chaperones].
Length = 412
Score = 31.0 bits (70), Expect = 0.57
Identities = 12/42 (28%), Positives = 21/42 (50%)
Query: 205 LKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEIM 246
LKK +I+ L+++I E N E + E + + +IM
Sbjct: 88 LKKNEEKIEELDERIREKEEDNGETEGSEADRNIAEYYCQIM 129
>gnl|CDD|221973 pfam13195, DUF4011, Protein of unknown function (DUF4011). This
family of proteins is found in archaea and bacteria.
Many members are annotated as being putative DNA
helicase-related proteins.
Length = 154
Score = 30.3 bits (69), Expect = 0.63
Identities = 23/90 (25%), Positives = 37/90 (41%), Gaps = 10/90 (11%)
Query: 124 NPIPGLPPAPSELNFDNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPP 183
N + P+ S + P+ LE + K + T++ H L
Sbjct: 9 NRLLNFKPSKSSIPLICPDPDLLEDLLSGDKLLIENRTLEDLHIELAEEALA-------- 60
Query: 184 APSELNFDNLSPEELEKRIKNLKKKVREIK 213
EL L+PEEL+KR++NL +K R +
Sbjct: 61 -DKELQTL-LTPEELQKRLRNLYRKARTLL 88
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 31.0 bits (71), Expect = 0.64
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 9/67 (13%)
Query: 197 ELEKRIKNLKKKVREIKTLEQKIESGEIK---------NPEKDQLEKLQRKPDLLSEIMA 247
EL+ R + + KK+ EI ++ +I IK + +++ L++L+ K L A
Sbjct: 23 ELKNRKEEVYKKIPEIAEIDDEIAKLGIKLSRAILKNPDKKEETLKELKEKITDLRVKKA 82
Query: 248 LKLSLHG 254
L +G
Sbjct: 83 ELLVSNG 89
>gnl|CDD|237255 PRK12900, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1025
Score = 30.9 bits (70), Expect = 0.73
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 190 FDNLSPEELEKRIKNLKKKVRE-IKTLEQKI--ESGEIKNPE--KDQLEKLQRKPDLLSE 244
+LS + L ++ LK +VR ++ +EQK ++ NP+ ++ E + + D L++
Sbjct: 34 LASLSDDALREKGMELKSRVRGALEPIEQKKKDLEKKLDNPDISLEEAESINEELDTLAK 93
>gnl|CDD|214610 smart00312, PX, PhoX homologous domain, present in p47phox and
p40phox. Eukaryotic domain of unknown function present
in phox proteins, PLD isoforms, a PI3K isoform.
Length = 105
Score = 29.2 bits (66), Expect = 0.83
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 122 PQNPIPGLPPAPSELNFDNLSPEELEKRIKNLKKKVREITVQVTHPVEMPR 172
P++ +P LP +N S E +EKR + L+K ++ + + HP +
Sbjct: 49 PRSILPPLPGKKLFGRLNNFSEEFIEKRRRGLEKYLQSL---LNHPELINH 96
>gnl|CDD|118308 pfam09776, Mitoc_L55, Mitochondrial ribosomal protein L55. Members
of this family are involved in mitochondrial biogenesis
and G2/M phase cell cycle progression. They form a
component of the mitochondrial ribosome large subunit
(39S) which comprises a 16S rRNA and about 50 distinct
proteins.
Length = 116
Score = 29.3 bits (66), Expect = 0.89
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 188 LNFDNLSPEELEKRIKNLKKKVREIKTLEQKIE 220
L+ D LSPEE R+ K+K + T+E+++E
Sbjct: 72 LDLDTLSPEERRARL--RKRKPKSKLTIEEELE 102
>gnl|CDD|227657 COG5354, COG5354, Uncharacterized protein, contains Trp-Asp (WD)
repeat [General function prediction only].
Length = 561
Score = 30.2 bits (68), Expect = 1.1
Identities = 28/110 (25%), Positives = 53/110 (48%), Gaps = 11/110 (10%)
Query: 141 LSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPE-ELE 199
L+ E +K +K + + P E + + + AP + PE E
Sbjct: 460 LTIESAKKYVKPSRHRFV--------PFEKAVIMEADSANRSSAPRKKELVEQWPEYSDE 511
Query: 200 KRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEIMALK 249
+I++L KK+R I+ L++++ SGE E Q+ K++ + ++LSE+ L
Sbjct: 512 DKIRSLLKKLRAIEALKERMRSGE--ELEVIQVNKIETEEEVLSELKELV 559
>gnl|CDD|180339 PRK05988, PRK05988, formate dehydrogenase subunit gamma;
Validated.
Length = 156
Score = 29.5 bits (67), Expect = 1.1
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 68 PIPGLVILDA--DDLGYVPQDEVPL 90
L IL A D+ GYVP+D VP+
Sbjct: 22 EGALLPILHAIQDEFGYVPEDAVPV 46
>gnl|CDD|223520 COG0443, DnaK, Molecular chaperone [Posttranslational modification,
protein turnover, chaperones].
Length = 579
Score = 30.4 bits (69), Expect = 1.1
Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 8/97 (8%)
Query: 141 LSPEELEKRIKN------LKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLS 194
LS EE+E+ +++ L KK RE+ + +L+ +LK
Sbjct: 483 LSDEEIERMVEDAEANAALDKKFRELVEARNEAESL--IYSLEKALKEIVKVSEEEKEKI 540
Query: 195 PEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQ 231
E + + L+ + EIK ++++ K EK
Sbjct: 541 EEAITDLEEALEGEKEEIKAKIEELQEVTQKLAEKKY 577
>gnl|CDD|148614 pfam07106, TBPIP, Tat binding protein 1(TBP-1)-interacting protein
(TBPIP). This family consists of several eukaryotic
TBP-1 interacting protein (TBPIP) sequences. TBP-1 has
been demonstrated to interact with the human
immunodeficiency virus type 1 (HIV-1) viral protein Tat,
then modulate the essential replication process of HIV.
In addition, TBP-1 has been shown to be a component of
the 26S proteasome, a basic multiprotein complex that
degrades ubiquitinated proteins in an ATP-dependent
fashion. Human TBPIP interacts with human TBP-1 then
modulates the inhibitory action of human TBP-1 on
HIV-Tat-mediated transactivation.
Length = 169
Score = 29.6 bits (67), Expect = 1.2
Identities = 28/102 (27%), Positives = 49/102 (48%), Gaps = 17/102 (16%)
Query: 138 FDNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELN--FDNLSP 195
F+ S EEL K L ++ E+ ++ L EL +L+
Sbjct: 66 FELPSDEELNK----LDMEIEELR----------EEVQLLKQDCSTLEIELKSLTSDLTT 111
Query: 196 EELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQR 237
EEL++ I+ LKK+VREI+ + +E G K +++EK+++
Sbjct: 112 EELQEEIQELKKEVREIEEKLESLEEG-WKPVTPEEMEKVKK 152
>gnl|CDD|153335 cd07651, F-BAR_PombeCdc15_like, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Schizosaccharomyces pombe
Cdc15, and similar proteins. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. This subfamily is composed of
Schizosaccharomyces pombe Cdc15 and Imp2, and similar
proteins. These proteins contain an N-terminal F-BAR
domain and a C-terminal SH3 domain. S. pombe Cdc15 and
Imp2 play both distinct and overlapping roles in the
maintenance and strengthening of the contractile ring at
the division site, which is required in cell division.
Cdc15 is a component of the actomyosin ring and is
required in normal cytokinesis. Imp2 colocalizes with
the medial ring during septation and is required for
normal septation. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
Length = 236
Score = 29.6 bits (67), Expect = 1.3
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 201 RIKNLKKKVREIKTLEQKIESGEIKNPEKD---QLEKLQRKPDLLSEIMALKLSLH 253
RIK+ + + E+++ + E I E++ +LEKL RK SE LK SL
Sbjct: 13 RIKDSLRTLEELRSFYK--ERASI---EEEYAKRLEKLSRKSLGGSEEGGLKNSLD 63
>gnl|CDD|236326 PRK08655, PRK08655, prephenate dehydrogenase; Provisional.
Length = 437
Score = 30.0 bits (68), Expect = 1.3
Identities = 27/113 (23%), Positives = 40/113 (35%), Gaps = 35/113 (30%)
Query: 136 LNFDNLSPEELEK-RIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLS 194
N LS +EL + + KNL+K VR+I+V
Sbjct: 340 SNIRLLSEKELREWKKKNLEKYVRDISVLFP-------------------------KGAD 374
Query: 195 PEELEKRIKNLKKKVR-EIKTLEQ--KIESG------EIKNPEKDQLEKLQRK 238
PE + + NLK EI + +IE G I K+ LE ++
Sbjct: 375 PEVILDLLDNLKHVFDIEIIDVYSGKQIEEGYLSVTFRITVFGKEDLENVEEI 427
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 30.1 bits (69), Expect = 1.3
Identities = 14/40 (35%), Positives = 28/40 (70%), Gaps = 2/40 (5%)
Query: 196 EELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKL 235
EELEK+ K L++K +E++ E+++E E+ + +LE++
Sbjct: 110 EELEKKEKELEQKQQELEKKEEELE--ELIEEQLQELERI 147
Score = 29.7 bits (68), Expect = 1.4
Identities = 13/55 (23%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 196 EELEKRIKNLKKKVREIKTLEQKIES--GEIKNPEKDQLEKLQRKPDLLSEIMAL 248
E L+++++ L+K+ E++ E+++E E++ E++ E ++ + L I L
Sbjct: 96 ENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELERISGL 150
>gnl|CDD|214738 smart00595, MADF, subfamily of SANT domain.
Length = 89
Score = 28.1 bits (63), Expect = 1.5
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 192 NLSPEELEKRIKNLKKK-VREIKTLEQKIESGEIK 225
LS EE +KR KNL+ + RE+K L+ G K
Sbjct: 38 GLSVEECKKRWKNLRDRYRRELKRLQNGKSGGGKK 72
>gnl|CDD|227512 COG5185, HEC1, Protein involved in chromosome segregation,
interacts with SMC proteins [Cell division and
chromosome partitioning].
Length = 622
Score = 30.0 bits (67), Expect = 1.5
Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 11/87 (12%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEK--- 200
E E+ IK L+ + E+ Q+ Q L + EL+ N+ ++L K
Sbjct: 340 ELKEEEIKALQSNIDELHKQLRKQGISTEQFELMNQEREKLTRELDKINIQSDKLTKSVK 399
Query: 201 --------RIKNLKKKVREIKTLEQKI 219
K+L+K +R+ +L Q I
Sbjct: 400 SRKLEAQGIFKSLEKTLRQYDSLIQNI 426
>gnl|CDD|220716 pfam10359, Fmp27_WPPW, RNA pol II promoter Fmp27 protein domain.
Fmp27_WPPW is a conserved domain of a family of proteins
involved in RNA polymerase II transcription initiation.
It contains characteristic HQR and WPPW sequence motifs.
and is towards the C-terminal in members which contain
Fmp27_SW pfam10305.
Length = 470
Score = 30.0 bits (68), Expect = 1.6
Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 16/78 (20%)
Query: 146 LEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIKNL 205
LE+R+K L+++++++ +L+ L+ EL D EELE+ + L
Sbjct: 166 LEERLKQLEEQIKKL----------EEKLD---DLELNDTEELQSDL---EELEEELSVL 209
Query: 206 KKKVREIKTLEQKIESGE 223
K+++ ++ L + +E E
Sbjct: 210 KERLEFLEKLLEDLERSE 227
Score = 28.0 bits (63), Expect = 5.4
Identities = 15/57 (26%), Positives = 33/57 (57%), Gaps = 12/57 (21%)
Query: 198 LEKRIKNLKKKVREIKTLEQKIESGEIKNPE---------KDQLEKLQRKPDLLSEI 245
LE+R+K L++ +IK LE+K++ E+ + E +++L L+ + + L ++
Sbjct: 166 LEERLKQLEE---QIKKLEEKLDDLELNDTEELQSDLEELEEELSVLKERLEFLEKL 219
>gnl|CDD|222409 pfam13837, Myb_DNA-bind_4, Myb/SANT-like DNA-binding domain. This
presumed domain appears to be related to other
Myb/SANT-like DNA binding domains. In particular
pfam10545 seems most related. This family is greatly
expanded in plants and appears in several proteins
annotated as transposon proteins.
Length = 84
Score = 28.0 bits (63), Expect = 1.6
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 186 SELNFDNLSPEELEKRIKNLKKKVREIKTLEQKIES 221
+E + N S E+ +++ KNLKKK ++ K + S
Sbjct: 43 AERGY-NRSAEQCKEKWKNLKKKYKKEKESNKGSGS 77
>gnl|CDD|218845 pfam05991, NYN_YacP, YacP-like NYN domain. This family consists of
bacterial proteins related to YacP. This family is
uncharacterized functionally, but it has been suggested
that these proteins are nucleases due to them containing
a NYN domain. NYN (for N4BP1, YacP-like Nuclease)
domains were discovered by Anantharaman and Aravind.
Based on gene neighborhoods it was suggested that the
bacterial YacP proteins interact with the Ribonuclease
III and TrmH methylase in a processome complex that
catalyzes the maturation of rRNA and tRNA.
Length = 165
Score = 29.1 bits (66), Expect = 1.7
Identities = 12/45 (26%), Positives = 23/45 (51%)
Query: 193 LSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQR 237
+S EL + +K +KK+R+ +K + + LEKL++
Sbjct: 118 ISSRELAEEVKRAEKKIRKKAEKRRKSRKKYLDRLSDEVLEKLEK 162
>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 = 30.0 bits (68), Expect = 1.7
Identities = 29/112 (25%), Positives = 50/112 (44%), Gaps = 15/112 (13%)
Query: 148 KRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRI----K 203
R++ L++++ E+ ++ E +L + +L L ELE+ I K
Sbjct: 232 LRLEELREELEELQEELK---EAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQK 288
Query: 204 NLKKKVREIKTLEQKIE--SGEIKNPEKD------QLEKLQRKPDLLSEIMA 247
L EI LEQ+ + + N E+ QLE+L+ K D L+E +A
Sbjct: 289 ELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELA 340
>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA
Topoisomerase I (eukaryota), DNA topoisomerase V,
Vaccina virus topoisomerase, Variola virus
topoisomerase, Shope fibroma virus topoisomeras.
Length = 391
Score = 29.6 bits (67), Expect = 1.8
Identities = 23/94 (24%), Positives = 48/94 (51%), Gaps = 4/94 (4%)
Query: 143 PEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDN----LSPEEL 198
+ EK ++ L++K++ + Q+ +M + LK S+ DN +E
Sbjct: 272 SKTHEKSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEK 331
Query: 199 EKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQL 232
+K K +KK ++I+ LE++IE E++ +K++
Sbjct: 332 KKEKKKEEKKKKQIERLEERIEKLEVQATDKEEN 365
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 29.5 bits (67), Expect = 1.9
Identities = 30/140 (21%), Positives = 55/140 (39%), Gaps = 30/140 (21%)
Query: 140 NLSPEELEKRIKNLKKKVREITVQVTHP---VEMPRQLNLKVSLKPPAPSELNFDNLS-- 194
L E L + I L ++I P +E+ +K+ + A E + +
Sbjct: 320 KLDIERLYRMIDILNDAQQQIK-WTNQPRIYLEV---ALVKLCEQAAASPEYDTELEVLL 375
Query: 195 --PEELEKRIKNLK--------------KKVREIKTLEQKIESGEI----KNPEKDQLEK 234
E+LE+ +K LK K+ ++ K + K+ G+I K + LE
Sbjct: 376 QRVEQLEQELKQLKAQPVGVAPEQKEKKKEKKKNKKKKYKVPRGKIYKVLKEATRQDLEL 435
Query: 235 LQRK-PDLLSEIMALKLSLH 253
L+ ++L + A + SL
Sbjct: 436 LKNVWGEILESLKAQRKSLR 455
>gnl|CDD|129371 TIGR00270, TIGR00270, TIGR00270 family protein. [Hypothetical
proteins, Conserved].
Length = 154
Score = 28.7 bits (64), Expect = 2.0
Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 6/76 (7%)
Query: 189 NFDNLSPEELEKR---IKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQR--KPDLLS 243
++ + E EKR + L KK++E ++L +KIE+ EI+ PE +EKL++ K L
Sbjct: 69 DYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIE-PEPKVVEKLEKLLKIKLRE 127
Query: 244 EIMALKLSLHGEEGEG 259
++ +K+ G + G
Sbjct: 128 QVPEIKIEKSGRKSLG 143
>gnl|CDD|222254 pfam13598, DUF4139, Domain of unknown function (DUF4139). This
family is usually found at the C-terminus of proteins.
Length = 264
Score = 29.1 bits (66), Expect = 2.0
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 150 IKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELN 189
+ NL K +TV+V + + R ++KV L P ++
Sbjct: 197 VTNLHK--EPVTVRVEDQLPVSRDEDIKVELLAPPEPAVD 234
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 29.1 bits (65), Expect = 2.2
Identities = 11/53 (20%), Positives = 29/53 (54%)
Query: 186 SELNFDNLSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRK 238
L +E ++R++ L+K++ E++ + +E + +K +LE+L+ +
Sbjct: 143 ERLEELKFKRKEKKERLEELEKELEELEDEKDLLEKLLEEKEKKKELEELKEE 195
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 29.3 bits (66), Expect = 2.2
Identities = 31/124 (25%), Positives = 57/124 (45%), Gaps = 34/124 (27%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQL-NLKVSLKPPAPSELNFDNLSPEELEKRI 202
E LE+ LK+++ E+ R++ L+ L E + +
Sbjct: 432 ERLEEENSELKRELE----------ELKREIEKLESEL---------------ERFRREV 466
Query: 203 KNLKKKVREIKTLEQKIESGEIKNPEKDQ-LEKLQRKPDLLSEIMALKLSLHGEEGEGEG 261
++ +K REI+ +++IE E + EK + +E+L+RK L ++ L+LS G+G
Sbjct: 467 RDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLAELRKMRKLELS-------GKG 519
Query: 262 THAK 265
T K
Sbjct: 520 TPVK 523
>gnl|CDD|232973 TIGR00433, bioB, biotin synthase. Catalyzes the last step of the
biotin biosynthesis pathway. All members of the seed
alignment are in the immediate gene neighborhood of a
bioA gene [Biosynthesis of cofactors, prosthetic groups,
and carriers, Biotin].
Length = 296
Score = 29.0 bits (66), Expect = 2.3
Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 11/53 (20%)
Query: 111 LDPSHVKKPVNPQNPIPGLPPAPSELNFDNLSPEELEK-----RIKNLKKKVR 158
LD V P+N PIPG P + L PEE + R ++R
Sbjct: 200 LDVDSV--PINFLVPIPGTPLE----DAPPLDPEECLRTIALFRFIMPDAEIR 246
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 29.6 bits (67), Expect = 2.3
Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 11/65 (16%)
Query: 185 PSELNFDNLSPEELEKRIKNLKKKVREIKTLEQKIESGEIKN----PEKDQLEKLQRKPD 240
P+ F NLSPE L + N + LE +I E++ P + R PD
Sbjct: 557 PNVCIFGNLSPETLVGVVVNDNR-------LEAEINKQELRRKYPYPRYIYVHCEPRSPD 609
Query: 241 LLSEI 245
L+SEI
Sbjct: 610 LVSEI 614
>gnl|CDD|224958 COG2047, COG2047, Uncharacterized protein (ATP-grasp superfamily)
[General function prediction only].
Length = 258
Score = 28.9 bits (65), Expect = 2.3
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 196 EELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKD 230
E LE+R K +++ + ++K +E+ E+ E K E+D
Sbjct: 219 EALEERAKEMEEIIEKLKEMEEMQEAQEPKPGEED 253
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 29.3 bits (66), Expect = 2.3
Identities = 31/119 (26%), Positives = 53/119 (44%), Gaps = 19/119 (15%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIK 203
EE EK I+ LK ++ E+ ++ E L LK + EELE I
Sbjct: 263 EEAEKEIEELKSELEELREELEELQE--ELLELKEEI---------------EELEGEIS 305
Query: 204 NLKKKVREIKTLEQKIESGEIKNPEK--DQLEKLQRKPDLLSEIMALKLSLHGEEGEGE 260
L++++ E++ +++E + EK E+L+ + LL E+ L L + E E
Sbjct: 306 LLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELE 364
Score = 27.8 bits (62), Expect = 7.9
Identities = 29/118 (24%), Positives = 56/118 (47%), Gaps = 29/118 (24%)
Query: 134 SELNFDNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNL 193
EL E LE+ I+ L++++ E+ +L+
Sbjct: 814 RELESLEQRRERLEQEIEELEEEIEELE------------------------EKLDELEE 849
Query: 194 SPEELEKRIKNLKKKVREIKTLEQKIES--GEIKNPEKDQLEKLQRKPDLLSEIMALK 249
EELEK ++ LK+++ E++ ++++E E++ EK++LE+ R+ L SE+ LK
Sbjct: 850 ELEELEKELEELKEELEELEAEKEELEDELKELEE-EKEELEEELRE--LESELAELK 904
Score = 27.4 bits (61), Expect = 9.4
Identities = 25/111 (22%), Positives = 52/111 (46%), Gaps = 6/111 (5%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIK 203
E+LE+ +K+LK ++R + + +L ++ EL E+L+ R++
Sbjct: 684 EKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEE---LKRELAALEEELEQLQSRLE 740
Query: 204 NLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQ-RKPDLLSEIMALKLSLH 253
L++++ E++ E+ E E +++LE L+ L EI L+
Sbjct: 741 ELEEELEELE--EELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQ 789
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 29.3 bits (67), Expect = 2.4
Identities = 8/37 (21%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 194 SPEELEKRIKNLKKKVR----EIKTLEQKIESGEIKN 226
P EL +R++ L ++++ E++ L+ K+ + +
Sbjct: 713 KPSELPERVEALLEELKELEKELEQLKAKLAAAAAGD 749
>gnl|CDD|129266 TIGR00162, TIGR00162, TIGR00162 family protein. This model
represents one out of two closely related ortholgous
sets of proteins that, so far, are found only in but are
universal among the Archaea. This ortholog set includes
MJ1210 from Methanococcus jannaschii and AF0525 from
Archaeoglobus fulgidus while excluding MJ0106 and AF1251
[Hypothetical proteins, Conserved].
Length = 188
Score = 28.7 bits (64), Expect = 2.5
Identities = 13/39 (33%), Positives = 26/39 (66%), Gaps = 1/39 (2%)
Query: 193 LSPEELEKRIKNLKKKVREIKTLEQK-IESGEIKNPEKD 230
+S E LE+R K ++K + +IK +E++ ++ + K E+D
Sbjct: 145 VSVEALEERAKEMEKIIAKIKEMEEEMVQQWKAKPSEED 183
>gnl|CDD|236381 PRK09108, PRK09108, type III secretion system protein HrcU;
Validated.
Length = 353
Score = 28.9 bits (65), Expect = 2.5
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 173 QLNLKVSLKPPAPSELNFDNLSPEELEKRIKNLKKKVREIKTL 215
Q L++SLKP P FD L+P K+I +L+ + +K +
Sbjct: 106 QTGLQISLKPVMP---KFDALNPAAGLKKIFSLRSLIELVKMI 145
>gnl|CDD|176455 cd01701, PolY_Rev1, DNA polymerase Rev1. Rev1 is a translesion
synthesis (TLS) polymerase found in eukaryotes.
Translesion synthesis is a process that allows the
bypass of a variety of DNA lesions. TLS polymerases
lack proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Rev1 has both
structural and enzymatic roles. Structurally, it is
believed to interact with other nonclassical polymerases
and replication machinery to act as a scaffold.
Enzymatically, it catalyzes the specific insertion of
dCMP opposite abasic sites. Rev1 interacts with the
Rev7 subunit of the B-family TLS polymerase Pol zeta
(Rev3/Rev7). Rev1 is known to actively promote the
introduction of mutations, potentially making it a
significant target for cancer treatment.
Length = 404
Score = 29.2 bits (66), Expect = 2.5
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 144 EELEKRIKNLKKKVREITVQV-----THPVEMP 171
EEL KR++ R+IT+++ P+E P
Sbjct: 317 EELSKRLEESNVTGRQITLKLMKRAPGAPIEPP 349
>gnl|CDD|221919 pfam13094, CENP-Q, CENP-A-nucleosome distal (CAD) centromere
subunit. CENP-Q is one of the components that assembles
onto the CENP-A-nucleosome distal (CAD) centromere. The
centromere, which is the basic element of chromosome
inheritance, is epigenetically determined in mammals.
CENP-A, the centromere-specific histone H3 variant,
assembles an array of nucleosomes and it is this that
seems to be the prime candidate for specifying
centromere identity. CENP-A nucleosomes directly recruit
a proximal CENP-A nucleosome associated complex (NAC)
comprised of CENP-M, CENP-N and CENP-T, CENP-U(50),
CENP-C and CENP-H. Assembly of the CENP-A NAC at
centromeres is dependent on CENP-M, CENP-N and CENP-T.
Additionally, there are seven other subunits which make
up the CENP-A-nucleosome distal (CAD) centromere,
CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and
CENP-S, also assembling on the CENP-A NAC. Fta7 is the
equivalent component of the fission yeast Sim4 complex.
Length = 159
Score = 28.5 bits (64), Expect = 2.6
Identities = 23/104 (22%), Positives = 41/104 (39%), Gaps = 16/104 (15%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAP-------SELNFDNLSPE 196
+ELEK K L+++ E + + + R L +V + SE NF
Sbjct: 65 QELEKNAKALEREREE---ESKNLHPVLRLLESEVLEENELLQDSLLELSERNFSPNLDP 121
Query: 197 ELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPD 240
EL +K L K + ++ +++ + LE+L D
Sbjct: 122 ELLDLLKQLNKHLESLQGNLEQLAG------LVEALERLYAALD 159
>gnl|CDD|218675 pfam05648, PEX11, Peroxisomal biogenesis factor 11 (PEX11). This
family consists of several peroxisomal biogenesis factor
11 (PEX11) proteins from several eukaryotic species. The
PEX11 peroxisomal membrane proteins promote peroxisome
division in multiple eukaryotes.
Length = 225
Score = 28.8 bits (65), Expect = 2.8
Identities = 9/50 (18%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 204 NLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRK-PDLLSEIMALKLSL 252
+L + +RE++ L++K + + + + + ++ +L + A L L
Sbjct: 136 SLVRDLRELRQLQEKEKKLKKEKDSEGESTSERKLLKKILKKRPAALLDL 185
>gnl|CDD|132166 TIGR03122, one_C_dehyd_C, formylmethanofuran dehydrogenase subunit
C. Members of this largely archaeal protein family are
subunit C of the formylmethanofuran dehydrogenase.
Nomenclature in some bacteria may reflect inclusion of
the formyltransferase described by TIGR03119 as part of
the complex, and therefore call this protein
formyltransferase/hydrolase complex Fhc subunit C. Note
that this model does not distinguish tungsten (FwdC)
from molybdenum-containing (FmdC) forms of this enzyme.
Length = 260
Score = 28.8 bits (65), Expect = 2.9
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 11/60 (18%)
Query: 176 LKVSLKPPAPSELNFDNLSPEELEKRIKNLKKKVREIKTLE-----QKIESGEIKNPEKD 230
L ++LK L D ++P+ L K EI LE + + G++ E D
Sbjct: 1 LTLTLKKEPSIPLEADPITPDNL------AGKSPEEIAALELQYGNRTVPLGDLFEVEGD 54
>gnl|CDD|217457 pfam03255, ACCA, Acetyl co-enzyme A carboxylase carboxyltransferase
alpha subunit. Acetyl co-enzyme A carboxylase
carboxyltransferase is composed of an alpha and beta
subunit.
Length = 145
Score = 28.0 bits (63), Expect = 2.9
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 197 ELEKRIKNLKKKVREIKTLEQKIE---SGEIKNPEKDQLEKLQRK 238
E EK + L+ K+ E++ L +K + S EI EK +L+KL+R+
Sbjct: 4 EFEKPLAELEAKIDELRKLARKNDVDVSDEIHRLEK-KLDKLKRE 47
>gnl|CDD|184628 PRK14331, PRK14331, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 437
Score = 29.0 bits (65), Expect = 2.9
Identities = 33/161 (20%), Positives = 59/161 (36%), Gaps = 41/161 (25%)
Query: 140 NLSPEELEKRIKNLKKKVREI--------------------TVQVTHPVEMPRQLNLKVS 179
+ EE ++I+ LK+ + +I T+ V VE + + K S
Sbjct: 276 GYTKEEYLEKIELLKEYIPDITFSTDIIVGFPTETEEDFEETLDVLKKVEFEQVFSFKYS 335
Query: 180 LKPPAPSELNFDNLSPEELEKRIKNL--------KKKVREIKTLEQKIESGEIKNPEK-- 229
+P P+ E KR+ L KK + Q++ E K K
Sbjct: 336 PRPGTPAAYMEGQEPDEVKTKRMNRLLELQKEITFKKALSYEGTVQEVLVEEEKEGNKLI 395
Query: 230 -----DQLEKLQRKPDLLSEIMALKL------SLHGEEGEG 259
++ ++ ++L +I+ +K+ SL GE EG
Sbjct: 396 GRTRTNKWVSIEGSQEMLGKIVKVKIIKSNPFSLEGEILEG 436
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 29.0 bits (65), Expect = 3.2
Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 15/95 (15%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIK 203
EELE++I+ L++ REI +L +L L E+L+ +
Sbjct: 284 EELEEKIERLEELEREIEELE-------EELEGLRALLEELEELL-------EKLKSLEE 329
Query: 204 NLKKKVREIKTLEQKIES-GEIKNPEKDQLEKLQR 237
L+K +++ LE ++E E KN LE+ +
Sbjct: 330 RLEKLEEKLEKLESELEELAEEKNELAKLLEERLK 364
Score = 28.6 bits (64), Expect = 4.5
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 196 EELEKRIKNLKKKVREIKTLEQKIESGEIKNPE--KDQLEKLQRKPDLLSEIMALKLSLH 253
E+ EK + LK+ ++E K +++E + E +D LE L+ + L ++ ++
Sbjct: 167 EKYEKLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQE 226
Query: 254 GEEGEGE 260
EE E E
Sbjct: 227 EEELEQE 233
>gnl|CDD|233996 TIGR02750, TraN_Ftype, type-F conjugative transfer system
mating-pair stabilization protein TraN. TraN is a large
cysteine-rich outer membrane protein involved in the
mating-pair stabilization (adhesin) component of the
F-type conjugative plamid transfer system. TraN is
believed to interact with the core type IV secretion
system apparatus through the TraV protein.
Length = 572
Score = 29.0 bits (65), Expect = 3.2
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 10/88 (11%)
Query: 38 GKQFANRQAAQSIPIGLDPSHVKKPVNPQNPIPGLVILDADDLGYVPQDEVPLYESKGKQ 97
G +A + A Q++ K P PG + GY PQ++ L K
Sbjct: 24 GVNWAKQAADQALD-------NIKGFCPDAACPGYTA-NPPQTGYYPQEDTGLNSQKTAA 75
Query: 98 FANRQAAQSIPIGLDPSHVKKPVNPQNP 125
AN A+++ + + + +NP P
Sbjct: 76 IANNDTAKAVQENFN--NGRPDLNPNTP 101
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 28.9 bits (65), Expect = 3.3
Identities = 12/57 (21%), Positives = 22/57 (38%)
Query: 193 LSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEIMALK 249
L I+NL+ K I L++ + + +++ + KL L LK
Sbjct: 911 LKKSLSSDLIENLEFKTELIARLKKLLNNIDLEEGPSIEYVKLPELNKLHEVESKLK 967
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 28.8 bits (65), Expect = 3.3
Identities = 24/103 (23%), Positives = 33/103 (32%), Gaps = 11/103 (10%)
Query: 53 GLDPSHVKKPVNPQNPIPGLVILDADDLGYVPQDEVPLYESKGKQFANRQAAQSIPIGLD 112
G + K P PQ P P P + +
Sbjct: 515 GSASNTAKTPPPPQKSPPPPAPT--------PPLPQPTATAPPPTPPPPPPTATQASSNA 566
Query: 113 PSHVKKPVNPQNPIPGLPPAPSELNFDNLSPEELEKRIKNLKK 155
P+ + +P PIP P PS + SPEE++K KNL
Sbjct: 567 PAQIPADSSPPPPIP-EEPTPSPTK--DSSPEEIDKAAKNLAD 606
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 28.8 bits (65), Expect = 3.4
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 187 ELNFDNLS-PEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEI 245
E+ D EEL++ + LK+ E++ +++ ++ K + EK ++ LL
Sbjct: 324 EVGVDFPELKEELKELEEELKELEEELEKIKKLLKKLPKKARGQLPPEKREQLEKLLETK 383
Query: 246 MALKLSLHGEEGE 258
L L E E
Sbjct: 384 EKLSEELEELEEE 396
>gnl|CDD|221229 pfam11799, IMS_C, impB/mucB/samB family C-terminal. These proteins
are involved in UV protection.
Length = 136
Score = 27.9 bits (62), Expect = 3.5
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFD---NLSPEELEK 200
EEL +R++ R +TV++ + + R LK K P + D + E LE+
Sbjct: 61 EELAERLRRRGLAARTVTVKLRYSDTVTRSRTLKTRQKRPTLPSNDTDELLEAALELLEQ 120
Query: 201 RIKNLKKKVREIKTL 215
++ L + I+ L
Sbjct: 121 ALRELFVRGAPIRLL 135
>gnl|CDD|149682 pfam08702, Fib_alpha, Fibrinogen alpha/beta chain family.
Fibrinogen is a protein involved in platelet aggregation
and is essential for the coagulation of blood. This
domain forms part of the central coiled coiled region of
the protein which is formed from two sets of three
non-identical chains (alpha, beta and gamma).
Length = 146
Score = 27.7 bits (62), Expect = 3.7
Identities = 17/95 (17%), Positives = 31/95 (32%), Gaps = 25/95 (26%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIK 203
E+LE + L V H + L+ K P++ ++ S + L K I+
Sbjct: 39 EDLENLLDQLANSTSSAHQYVKHIKDS-----LRGDQKQAQPNDNIYNAYS-KSLRKMIE 92
Query: 204 NLKKK-------------------VREIKTLEQKI 219
+ + +I+ LE I
Sbjct: 93 YILETKINTQESQIRVLQEVLRSNRSKIQRLEVDI 127
>gnl|CDD|239618 cd03556, L-fucose_isomerase, L-fucose isomerase (FucIase); FucIase
converts L-fucose, an aldohexose, to its ketose form,
which prepares it for aldol cleavage (similar to the
isomerization of glucose during glycolysis). L-fucose
(or 6-deoxy-L-galactose) is found in blood group
determinants as well as in various oligo- and
polysaccharides, and glycosides in mammals, bacteria and
plants.
Length = 584
Score = 28.6 bits (64), Expect = 3.9
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 10/47 (21%)
Query: 195 PEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDL 241
PEE EK + K+ +E GE +N + DQ ++ Q+ D
Sbjct: 218 PEEYEKALAWTKENCKE----------GEDENEKNDQKKREQKDKDW 254
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 28.7 bits (64), Expect = 4.0
Identities = 22/115 (19%), Positives = 56/115 (48%), Gaps = 5/115 (4%)
Query: 144 EELEKRIKNLKKKVREITVQV----THPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELE 199
E++K++ +L+ +++EI + ++ + R++ + + +E+ + + E+L
Sbjct: 590 NEIKKQLNDLESRLQEIEIGFPDDKSYIDKSIREIENEANNLNNKYNEIQENKILIEKLR 649
Query: 200 KRIKNLKKKVREIKTLEQKIESGEIK-NPEKDQLEKLQRKPDLLSEIMALKLSLH 253
+I N KK++ EI ++ ++ + N +D L+K ++ D A S
Sbjct: 650 GKIDNYKKQIAEIDSIIPDLKEITSRINDIEDNLKKSRKALDDAKANRARLESTI 704
>gnl|CDD|220404 pfam09789, DUF2353, Uncharacterized coiled-coil protein (DUF2353).
Members of this family of uncharacterized proteins have
no known function.
Length = 319
Score = 28.3 bits (63), Expect = 4.2
Identities = 33/129 (25%), Positives = 51/129 (39%), Gaps = 17/129 (13%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIK 203
E L+ R +NLKK RE+ + +M + K + +N + ++
Sbjct: 33 ETLQMRYRNLKKSERELELVAACQGDMKIKPGTKRQDLSQLLEKYREENQQLSTDVQELR 92
Query: 204 NLKKKVRE-IKTLEQKI-------------ESGEIKNPEKDQLEKLQRKPDLLSEIMALK 249
K +++ IK L Q I ES E +N QLEKL+ K L +
Sbjct: 93 QRKAELQGDIKLLRQTIAQQRVEFMGGGVRESFEERNDLVSQLEKLREKCKQLESDLR-- 150
Query: 250 LSLHGEEGE 258
SL E+ E
Sbjct: 151 -SLLDEKEE 158
>gnl|CDD|173832 cd00684, Terpene_cyclase_plant_C1, Plant Terpene Cyclases, Class 1.
This CD includes a diverse group of monomeric plant
terpene cyclases (Tspa-Tspf) that convert the acyclic
isoprenoid diphosphates, geranyl diphosphate (GPP),
farnesyl diphosphate (FPP), or geranylgeranyl
diphosphate (GGPP) into cyclic monoterpenes, diterpenes,
or sesquiterpenes, respectively; a few form acyclic
species. Terpnoid cyclases are soluble enzymes localized
to the cytosol (sesquiterpene synthases) or plastids
(mono- and diterpene synthases). All monoterpene and
diterpene synthases have restrict substrate specificity,
however, some sesquiterpene synthases can accept both
FPP and GPP. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions located on
opposite walls. These residues mediate binding of prenyl
diphosphates, via bridging Mg2+ ions (K+ preferred by
gymnosperm cyclases), inducing conformational changes
such that an N-terminal region forms a cap over the
catalytic core. Loss of diphosphate from the
enzyme-bound substrate (GPP, FPP, or GGPP) results in an
allylic carbocation that electrophilically attacks a
double bond further down the terpene chain to effect the
first ring closure. Unlike monoterpene, sesquiterene,
and macrocyclic diterpenes synthases, which undergo
substrate ionization by diphosphate ester scission,
Tpsc-like diterpene synthases catalyze cyclization
reactions by an initial protonation step producing a
copalyl diphosphate intermediate. These enzymes lack the
aspartate-rich sequences mentioned above. Most diterpene
synthases have an N-terminal, internal element (approx
210 aa) whose function is unknown.
Length = 542
Score = 28.3 bits (64), Expect = 4.5
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 188 LNFDNLSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLE---KLQR 237
L+ D +ELE+ I+ LK++VR+ +E E ++L +LQR
Sbjct: 19 LSSDYSEEDELEEEIEELKEEVRK------MLEDSEYPVDLFERLWLIDRLQR 65
>gnl|CDD|222689 pfam14335, DUF4391, Domain of unknown function (DUF4391). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 220 and
257 amino acids in length.
Length = 221
Score = 28.0 bits (63), Expect = 4.6
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 196 EELEKRIKNLKKKVREIKTLEQKIE 220
EELEK I LKKK+++ K +K+E
Sbjct: 185 EELEKEIAKLKKKLKKEKQFNRKVE 209
>gnl|CDD|234861 PRK00911, PRK00911, dihydroxy-acid dehydratase; Provisional.
Length = 552
Score = 28.5 bits (65), Expect = 4.7
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 192 NLSPEELEKRIKNLKKKVREIKT 214
+S EEL +R K + K
Sbjct: 508 LVSDEELARRRAAWKPPEPKYKR 530
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 28.4 bits (64), Expect = 4.9
Identities = 11/40 (27%), Positives = 24/40 (60%), Gaps = 6/40 (15%)
Query: 196 EELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKL 235
E++EK IK L++++ E++ +++E E ++LE
Sbjct: 96 EKIEKEIKELEEEISELENEIKELEQ------EIERLEPW 129
>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 = 28.4 bits (64), Expect = 4.9
Identities = 13/48 (27%), Positives = 27/48 (56%), Gaps = 8/48 (16%)
Query: 196 EELEKRIKNLKKKVRE-IKTLEQKIESGEIKNPEKDQLEKLQRKPDLL 242
+LEKR++N +K+ + ++ LE+++E E + E + +LL
Sbjct: 295 SDLEKRVENELEKLEKKLEKLEKELE-------EAENAENYRLYGELL 335
>gnl|CDD|216119 pfam00787, PX, PX domain. PX domains bind to phosphoinositides.
Length = 109
Score = 26.9 bits (60), Expect = 4.9
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 122 PQNPIPGLPPAPSELNFDNLSPEELEKRIKNLKKKVREITVQVTHPVEM 170
P IP LPP F S E +EKR K L++ ++ + + HP
Sbjct: 55 PGRIIPPLPPKKL---FGRFSEEFIEKRRKGLEEYLQRL---LQHPELS 97
>gnl|CDD|220803 pfam10545, MADF_DNA_bdg, Alcohol dehydrogenase transcription factor
Myb/SANT-like. The myb/SANT-like domain in Adf-1 (MADF)
is an approximately 80-amino-acid module that directs
sequence specific DNA binding to a site consisting of
multiple tri-nucleotide repeats. The MADF domain is
found in one or more copies in eukaryotic and viral
proteins and is often associated with the BESS domain.
It is likely that the MADF domain is more closely
related to the myb/SANT domain than it is to other HTH
domains.
Length = 84
Score = 26.5 bits (59), Expect = 5.3
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 186 SELNFDNLSPEELEKRIKNLKKK-VREIKTLEQKIESGEIKNPEKDQLEKLQ 236
EL D + EE +K+ KNL+ + RE++ + + SGE + E+L
Sbjct: 34 EELGED-VDVEECKKKWKNLRDRYRRELR--KIRSGSGESYKSKWYYYEELS 82
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 28.3 bits (64), Expect = 5.5
Identities = 14/54 (25%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 193 LSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEIM 246
L ++EK I++LK++ I +E ++ E ++ E++Q + D L +I+
Sbjct: 249 LDHLDIEKEIQDLKEQ---IDENLALLEELDLDEAE-EKNEEIQERIDQLYDIL 298
>gnl|CDD|221408 pfam12072, DUF3552, Domain of unknown function (DUF3552). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria, archaea and eukaryotes.
This domain is about 200 amino acids in length. This
domain is found associated with pfam00013, pfam01966.
This domain has a single completely conserved residue A
that may be functionally important.
Length = 201
Score = 27.5 bits (62), Expect = 5.7
Identities = 10/40 (25%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 196 EELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKL 235
E LE++ K L + ++++ E+++E E+ ++ +LE++
Sbjct: 106 ESLEEKEKELAARQQQLEEKEEELE--ELIEEQQQELERI 143
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 655
Score = 28.0 bits (63), Expect = 5.7
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 151 KNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIKNLKKKVR 210
+ ++K +R+I +L K + +LS +EL+K IK L+K+++
Sbjct: 583 QTIRKPIRDIL---------DIELKEKEDAAKKKKKGEDLSDLSKKELKKLIKQLEKEMK 633
Query: 211 E 211
+
Sbjct: 634 Q 634
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 140
Score = 27.2 bits (61), Expect = 5.8
Identities = 11/43 (25%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 196 EELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRK 238
+E +KR L+K +E++ L++K++ E EK +++
Sbjct: 25 KEFKKRQAELEKLEKELQKLKEKLQKDAATLSE-AAREKKEKE 66
>gnl|CDD|216477 pfam01397, Terpene_synth, Terpene synthase, N-terminal domain. It
has been suggested that this gene family be designated
tps (for terpene synthase). It has been split into six
subgroups on the basis of phylogeny, called tpsa-tpsf.
tpsa includes vetispiridiene synthase, 5-epi-
aristolochene synthase, and (+)-delta-cadinene synthase.
tpsb includes (-)-limonene synthase. tpsc includes
kaurene synthase A. tpsd includes taxadiene synthase,
pinene synthase, and myrcene synthase. tpse includes
kaurene synthase B. tpsf includes linalool synthase.
Length = 177
Score = 27.5 bits (62), Expect = 5.9
Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 11/40 (27%)
Query: 196 EELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKL 235
E+ +R+++LK++VR + + D LE+L
Sbjct: 17 EKCLERLESLKEEVR-----------KMLPSSYPDLLEQL 45
>gnl|CDD|149592 pfam08593, MUG2_C, Meiotically up-regulated glycoproteins
C-terminal. This is the C-terminal part of some
meiotically up-regulated gene products from fission
yeast. The actual function is not yet known but the
proteins are likely to be cell-surface glycoproteins.
Length = 94
Score = 26.6 bits (59), Expect = 6.1
Identities = 12/43 (27%), Positives = 18/43 (41%)
Query: 109 IGLDPSHVKKPVNPQNPIPGLPPAPSELNFDNLSPEELEKRIK 151
G + V P + P LPP S + D LS E+ + +
Sbjct: 15 NGYPATPVPFPNGEEPEQPLLPPIGSIQDIDILSKEQCSRYLP 57
>gnl|CDD|236473 PRK09348, glyQ, glycyl-tRNA synthetase subunit alpha; Validated.
Length = 283
Score = 27.8 bits (63), Expect = 6.2
Identities = 9/11 (81%), Positives = 10/11 (90%), Gaps = 1/11 (9%)
Query: 4 YIQPSRRP-DG 13
Y+QPSRRP DG
Sbjct: 55 YVQPSRRPTDG 65
>gnl|CDD|173862 cd08497, PBP2_NikA_DppA_OppA_like_14, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 491
Score = 27.9 bits (63), Expect = 6.7
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 9 RRPDGTFRKAIRV--KAGYVPQDEVPLYESKGKQFA 42
R RKA+ + +AG+ + L + G+ +
Sbjct: 314 TRTRFNLRKALELLAEAGWTVRGGDILVNADGEPLS 349
>gnl|CDD|223147 COG0069, GltB, Glutamate synthase domain 2 [Amino acid transport
and metabolism].
Length = 485
Score = 27.6 bits (62), Expect = 6.9
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 164 VTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIKNLKK 207
VT + R V L P P D S E+L + IK+LK+
Sbjct: 259 VTPEIAKTRGSPPGVGLISPPPHH---DIYSIEDLAQLIKDLKE 299
>gnl|CDD|181526 PRK08659, PRK08659, 2-oxoglutarate ferredoxin oxidoreductase
subunit alpha; Validated.
Length = 376
Score = 27.5 bits (62), Expect = 6.9
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 147 EKRIKNLKKKVREITV------QVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEK 200
E+ I+ L KKV+ I V Q++ VE KV EL ++PEE+ +
Sbjct: 315 EEAIRELAKKVKAIVVPEMNLGQMSLEVERVVNGRAKVEGINKIGGEL----ITPEEILE 370
Query: 201 RIKNLK 206
+IK +
Sbjct: 371 KIKEVA 376
>gnl|CDD|223895 COG0825, AccA, Acetyl-CoA carboxylase alpha subunit [Lipid
metabolism].
Length = 317
Score = 27.6 bits (62), Expect = 6.9
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 197 ELEKRIKNLKKKVREIKTLEQKIE---SGEIKNPEKDQLEKLQRKP 239
+ EK I L+ K+ E+K L ++ + S EI+ EK +L +L +K
Sbjct: 6 DFEKPIAELEAKIDELKALAEENDVDLSDEIERLEK-RLAELTKKI 50
>gnl|CDD|232969 TIGR00422, valS, valyl-tRNA synthetase. The valyl-tRNA synthetase
(ValS) is a class I amino acyl-tRNA ligase and is
particularly closely related to the isoleucyl tRNA
synthetase [Protein synthesis, tRNA aminoacylation].
Length = 861
Score = 27.7 bits (62), Expect = 7.0
Identities = 20/90 (22%), Positives = 38/90 (42%), Gaps = 6/90 (6%)
Query: 144 EELEKRIKNLKK--KVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKR 201
E L+ ++K E+ V + P + L + P + N + +EL +
Sbjct: 764 ERLKLNAVDIKGAINFSEVEVVIEKPEVTEAVVELVPGFEIIIPVK-GLINKA-KELARL 821
Query: 202 IKNLKKKVREIKTLEQKI--ESGEIKNPEK 229
K L K+ +E+ +E K+ E K P++
Sbjct: 822 QKQLDKEKKEVIRIEGKLENEGFVKKAPKE 851
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 27.2 bits (61), Expect = 7.0
Identities = 10/48 (20%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 191 DNLSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRK 238
LS E + + + L++K +E++ +Q + E++ +++ L+ + K
Sbjct: 70 ATLSEEARKAKQQELQQKQQELQQKQQAAQ-QELQQKQQELLQPIYDK 116
>gnl|CDD|234252 TIGR03545, TIGR03545, TIGR03545 family protein. This model
represents a relatively rare but broadly distributed
uncharacterized protein family, distributed in 1-2
percent of bacterial genomes, all of which have outer
membranes. In many of these genomes, it is part of a
two-gene pair.
Length = 555
Score = 27.8 bits (62), Expect = 7.0
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 194 SPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEIMALK 249
+P EL+K + K +E K +QKI+S K+ L+ K L +++ LK
Sbjct: 210 NPLELQKIKEEFDKLKKEGKADKQKIKS------AKNDLQND--KKQLKADLAELK 257
>gnl|CDD|236080 PRK07734, motB, flagellar motor protein MotB; Reviewed.
Length = 259
Score = 27.4 bits (61), Expect = 7.2
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 189 NFDNLSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPD 240
D LS ++ E K L E + ++K E+ K E ++L+ +Q+K D
Sbjct: 65 VKDFLSDQKPEDE-KELSASSLEAEQAKKKEEAEAKKKKEMEELKAVQKKID 115
>gnl|CDD|176475 cd08638, DNA_pol_A_theta, DNA polymerase theta is a low-fidelity
family A enzyme implicated in translesion synthesis and
in somatic hypermutation. DNA polymerase theta is a
low-fidelity family A enzyme implicated in translesion
synthesis (TLS) and in somatic hypermutation (SHM).
DNA-dependent DNA polymerases can be classified in six
main groups based upon phylogenetic relationships with
E. coli polymerase I (classA), E. coli polymerase II
(class B), E.coli polymerase III (class C),
euryarchaaeota polymerase II (class D), human polymerase
beta (class x), E. coli UmuC/DinB and eukaryotic RAP
30/Xeroderma pigmentosum variant (class Y). Family A
polymerase functions primarily to fill DNA gaps that
arise during DNA repair, recombination and replication.
Pol theta is an exception among family A polymerases and
generates processive single base substitutions. Family A
polymerase are found primarily in organisms related to
prokaryotes and include prokaryotic DNA polymerase I
(pol I) ,mitochondrial polymerase delta, and several
bacteriphage polymerases including those from
odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
have two functional domains located on the same
polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
Pol I uses its 5' nuclease activity to remove the
ribonucleotide portion of newly synthesized Okazaki
fragments and DNA polymerase activity to fill in the
resulting gap. Polymerase theta mostly has
amino-terminal helicase domain, a carboxy-terminal
polymerase domain and an intervening space region.
Length = 373
Score = 27.6 bits (62), Expect = 7.4
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 7/54 (12%)
Query: 194 SPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEIMA 247
PEELE++ L+ K++E LE++ ++ K+ LE+L+R L I+
Sbjct: 5 DPEELERQRALLQAKLKE---LEEEAY----RSTSKEVLEQLKRLHPLPKLILE 51
>gnl|CDD|219523 pfam07697, 7TMR-HDED, 7TM-HD extracellular. This entry represents
the extracellular domain of the 7TM-HD (7TM Receptors
with HD hydrolase).
Length = 218
Score = 27.3 bits (61), Expect = 7.4
Identities = 23/108 (21%), Positives = 45/108 (41%), Gaps = 4/108 (3%)
Query: 132 APSELNFDNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELN-F 190
P + D + LE+ I +L ++RE+ + R +L +S + + +
Sbjct: 36 VPPVYDIDPEVTQNLEEEINSLFDEIREVKASAEKAEKADRLKSLNLSTFQLSDEQWSTL 95
Query: 191 DNLSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRK 238
N E+L+ ++ + I L Q I G + K++ KLQ +
Sbjct: 96 LNADDEDLKLLEDAIRTALDRI--LSQGIREGLL-IEAKEEAAKLQLE 140
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 28.0 bits (63), Expect = 7.4
Identities = 29/127 (22%), Positives = 44/127 (34%), Gaps = 25/127 (19%)
Query: 131 PAPSELNFDNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSE--- 187
P E D EE EK + LK+ + I + + + LKV L E
Sbjct: 709 PEVDEELID----EEAEKEFELLKEIISAIR-NLRAEMNLSPSAPLKVVLVGSEELEDRL 763
Query: 188 ----------LNFDNLS-----PEELEKRIKNLKKKVREIKTLEQKI-ESGEIKNPEKDQ 231
N + L PEE + + L I + E+ EK +
Sbjct: 764 EANEDDIKGLANLEELEILSPDPEEPPVEVTAVVGGAELFLPLAGLIDLAAELARLEK-E 822
Query: 232 LEKLQRK 238
LEKL+++
Sbjct: 823 LEKLEKE 829
>gnl|CDD|215960 pfam00509, Hemagglutinin, Haemagglutinin. Hemagglutinin from
influenza virus causes membrane fusion of the viral
membrane with the host membrane. Fusion occurs after the
host cell internalises the virus by endocytosis. The
drop of pH causes release of a hydrophobic fusion
peptide and a large conformational change leading to
membrane fusion.
Length = 550
Score = 27.7 bits (62), Expect = 7.5
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 189 NFDNLSPE--ELEKRIKNLKKKVREIKT 214
F+ + E ELE+RI NL KKV + T
Sbjct: 390 QFEAIEKEFSELERRINNLNKKVDDGIT 417
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 27.6 bits (62), Expect = 7.6
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 134 SELNFDNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNL 193
EL FD EE+E+R+ LK R+ V + +E ++ +++ +L+
Sbjct: 290 DELEFDPNRLEEVEERLFALKSLARKYGVTIEDLLEYLDKIKEELA-------QLDNSEE 342
Query: 194 SPEELEKRIKNLKKKVREI 212
S E LEK +K LK ++ E
Sbjct: 343 SLEALEKEVKKLKAELLEA 361
>gnl|CDD|233073 TIGR00653, GlnA, glutamine synthetase, type I. Alternate name:
glutamate--ammonia ligase. This model represents the
dodecameric form, which can be subdivided into 1-alpha
and 1-beta forms. The phylogeny of the 1-alpha and
1-beta forms appears polyphyletic. E. coli,
Synechocystis PCC6803, Aquifex aeolicus, and the
crenarcheon Sulfolobus acidocaldarius have form 1-beta,
while Bacillus subtilis, Thermotoga maritima, and
various euryarchaea has form 1-alpha. The 1-beta
dodecamer from the crenarcheon Sulfolobus acidocaldarius
differs from that in E. coli in that it is not regulated
by adenylylation [Amino acid biosynthesis, Glutamate
family].
Length = 459
Score = 27.7 bits (62), Expect = 7.6
Identities = 30/98 (30%), Positives = 38/98 (38%), Gaps = 23/98 (23%)
Query: 83 VPQDEVPLYESKGKQFANRQAAQSIPIGLDPS----HVKKPVNPQNP--------IPGL- 129
VP E P+Y + + NR A IP +P + P NP + GL
Sbjct: 315 VPGYEAPVYLAYSAR--NRSALIRIPASGNPKAKRIEFRFPDPSANPYLAFAAMLMAGLD 372
Query: 130 -------PPAPSELNFDNLSPEEL-EKRIKNLKKKVRE 159
P P + N LSPEEL EK I L + E
Sbjct: 373 GIKNKIDPGEPVDKNLYELSPEELREKGIPQLPGSLEE 410
>gnl|CDD|234096 TIGR03031, cas_csx12, CRISPR-associated protein Cas9/Csx12, subtype
II-B/NMENI. Members of this family of CRISPR-associated
(cas) protein are found, so far, in CRISPR/cas loci in
Wolinella succinogenes DSM 1740, Legionella pneumophila
str. Paris, and Francisella tularensis, where the last
probably is an example of a degenerate CRISPR locus,
having neither repeats nor a functional Cas1. The
characteristic repeat length is 37 base pairs and period
is about 72. One region of this large protein shows
sequence similarity to pfam01844, HNH endonuclease
[Mobile and extrachromosomal element functions, Other].
Length = 802
Score = 27.6 bits (61), Expect = 7.7
Identities = 17/36 (47%), Positives = 20/36 (55%)
Query: 196 EELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQ 231
EE K+IK R KTLEQ IE EI+ +K Q
Sbjct: 718 EESLKKIKGSSSDDRRKKTLEQAIEKQEIQWKDKFQ 753
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 27.6 bits (62), Expect = 7.8
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 110 GLDPSHVKKPVNPQNPIPGLP----PAPSELNFDNLSPEELEKRIKNLKKKVRE 159
G+ P +KK + A E +S +ELEK IK L+K+++E
Sbjct: 583 GITPQTIKKKI-RDILDGEYEEDEYKAKIEKKASKMSKKELEKLIKKLEKEMKE 635
>gnl|CDD|224129 COG1208, GCD1, Nucleoside-diphosphate-sugar pyrophosphorylase
involved in lipopolysaccharide biosynthesis/translation
initiation factor 2B, gamma/epsilon subunits
(eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis,
outer membrane / Translation, ribosomal structure and
biogenesis].
Length = 358
Score = 27.7 bits (62), Expect = 7.8
Identities = 25/129 (19%), Positives = 50/129 (38%), Gaps = 22/129 (17%)
Query: 136 LNFDNLSPEELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSP 195
LN D L+ +L + ++ KKK T+ +T F +
Sbjct: 105 LNGDVLTDLDLSELLEFHKKKGALATIALTRV-----------------LDPSEFGVVET 147
Query: 196 EELEKRIKNLKKKVREIKTLEQKIESG-EIKNPE----KDQLEKLQRKPDLLSEIMALKL 250
++ + R+ ++K + I +G I +PE ++ E+ + +LL + A
Sbjct: 148 DDGDGRVVEFREKPGPEEPPSNLINAGIYIFDPEVFDYIEKGERFDFEEELLPALAAKGE 207
Query: 251 SLHGEEGEG 259
++G EG
Sbjct: 208 DVYGYVFEG 216
>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 = 27.7 bits (62), Expect = 7.8
Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 6/71 (8%)
Query: 197 ELEKRIKNLKKKVREIKT-LEQKIESGEIKNPEKDQLEKLQRKPDLLSEIMALKLSLHGE 255
E+E +I+ LKK++++++ +EQ E K E ++ + L + +
Sbjct: 92 EIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKN-----KFLDKAWKKLAKKYDS 146
Query: 256 EGEGEGTHAKY 266
Y
Sbjct: 147 NLSEALKGLNY 157
>gnl|CDD|144972 pfam01576, Myosin_tail_1, Myosin tail. The myosin molecule is a
multi-subunit complex made up of two heavy chains and
four light chains it is a fundamental contractile
protein found in all eukaryote cell types. This family
consists of the coiled-coil myosin heavy chain tail
region. The coiled-coil is composed of the tail from two
molecules of myosin. These can then assemble into the
macromolecular thick filament. The coiled-coil region
provides the structural backbone the thick filament.
Length = 859
Score = 27.7 bits (62), Expect = 8.4
Identities = 37/131 (28%), Positives = 59/131 (45%), Gaps = 19/131 (14%)
Query: 144 EELEKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPE-ELEKR- 201
+ LE+ K L+ +V+E+ V++ + LK K E L E + E+R
Sbjct: 710 QHLERLRKQLESQVKELQVRL----DEAEAAALKGGKKMIQKLEARVRELEAELDGEQRR 765
Query: 202 ----IKNLKKKVREIKTLEQKIESGEIKNPE--KDQLEKLQRKPDLLSEIMALKLSLHGE 255
KNL+K R +K L+ ++E + KN E +D ++KLQ K I K L
Sbjct: 766 HAETQKNLRKMERRVKELQFQVEE-DKKNLERLQDLVDKLQAK------IKTYKRQLEEA 818
Query: 256 EGEGEGTHAKY 266
E + +KY
Sbjct: 819 EEVAQINLSKY 829
>gnl|CDD|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
Length = 652
Score = 27.7 bits (63), Expect = 8.6
Identities = 26/107 (24%), Positives = 42/107 (39%), Gaps = 40/107 (37%)
Query: 110 GLDPSHVKKPVNPQNPIPGLPPAPSELNFDNLSPEELEKRIKNLKKKVREITVQVTHPVE 169
G+ P +KK + ++ + + D LS +ELEK IK L+K+++E
Sbjct: 583 GITPKTIKKKI--RDILDSVYKK------DKLSKKELEKLIKELEKQMKE---------- 624
Query: 170 MPRQLNLKVSLKPPAPSELNFDNLSPEE---LEKRIKNLKKKVREIK 213
A L F EE L IK LK+++ +
Sbjct: 625 --------------AAKNLEF-----EEAARLRDEIKELKEELLGLS 652
>gnl|CDD|238243 cd00427, Ribosomal_L29_HIP, Ribosomal L29 protein/HIP. L29 is a
protein of the large ribosomal Subunit. A homolog,
called heparin/heparan sulfate interacting protein
(HIP), has also been identified in mammals. L29 is
located on the surface of the large ribosomal subunit,
where it participates in forming a protein ring that
surrounds the polypeptide exit channel, providing
structural support for the ribosome. L29 is involved in
forming the translocon binding site, along with L19,
L22, L23, L24, and L31e. In addition, L29 and L23 form
the interaction site for trigger factor (TF) on the
ribosomal surface, adjacent to the exit tunnel. L29
forms numerous interactions with L23 and with the 23S
rRNA. In some eukaryotes, L29 is referred to as L35,
which is distinct from L35 found in bacteria and some
eukaryotes (primarily plastids and mitochondria). The
mammalian homolog, HIP, is found on the surface of many
tissues and cell lines. It is believed to play a role in
cell adhesion and modulation of blood coagulation. It
has also been shown to inhibit apoptosis in cancer
cells.
Length = 57
Score = 25.1 bits (56), Expect = 8.9
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 192 NLSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEK 229
S EEL++++ LKK E+ L + +G+++NP +
Sbjct: 5 EKSDEELQEKLDELKK---ELFNLRFQKATGQLENPHR 39
>gnl|CDD|234722 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
Length = 232
Score = 27.0 bits (61), Expect = 9.3
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 14/45 (31%)
Query: 202 IKNLKKKVREI--KTLEQKIESGEIKNPEKD----------QLEK 234
I+ L+K++ ++ K ++ I E+K PE D QLE+
Sbjct: 84 IEKLRKELEKLTGKPVQINIV--EVKKPELDAQLVAESIAQQLER 126
>gnl|CDD|219445 pfam07517, SecA_DEAD, SecA DEAD-like domain. SecA protein binds to
the plasma membrane where it interacts with proOmpA to
support translocation of proOmpA through the membrane.
SecA protein achieves this translocation, in association
with SecY protein, in an ATP dependent manner. This
domain represents the N-terminal ATP-dependent helicase
domain, which is related to the pfam00270.
Length = 381
Score = 27.1 bits (61), Expect = 9.3
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 23/71 (32%)
Query: 147 EKRIKNLKKKVREITVQVTHPVEMPRQLNLKVSLKPPAPSELNFDNLSPEELEKRIKNLK 206
E+ +K L+K V +I +L+ + LS EEL + + L+
Sbjct: 10 ERDLKRLRKIVDQI-----------------NALEE------EYKALSDEELRAKTQELR 46
Query: 207 KKVREIKTLEQ 217
K++ +TL+
Sbjct: 47 KRLANGETLDD 57
>gnl|CDD|223988 COG1060, ThiH, Thiamine biosynthesis enzyme ThiH and related
uncharacterized enzymes [Coenzyme metabolism / General
function prediction only].
Length = 370
Score = 27.3 bits (61), Expect = 9.3
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 16/80 (20%)
Query: 141 LSPEELEKRIKNLKKK-VREITVQV-THPVEMP----------RQLNLKVSLKPPAPSEL 188
LSPEE+ + ++ K+ + E+ + HP ++ + + + E+
Sbjct: 90 LSPEEILEEVREAVKRGITEVLIVGGEHPELSLEYYEELFRTIKEEFPDLHIHALSAGEI 149
Query: 189 NF----DNLSPEELEKRIKN 204
F LS EE+ KR+K
Sbjct: 150 LFLAREGGLSYEEVLKRLKE 169
>gnl|CDD|240411 PTZ00419, PTZ00419, valyl-tRNA synthetase-like protein;
Provisional.
Length = 995
Score = 27.3 bits (61), Expect = 9.8
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 197 ELEKRIKNLKKKVREIKTLEQKIESG--EIKNPEKDQLEKLQRKPDLLSEIMAL 248
EL K K L K + +++ +KI E K PE + ++ +L EI L
Sbjct: 930 ELAKLEKKLAKLQKSLESYLKKISIPNYEDKVPEDVRKLNDEKIDELNEEIKQL 983
>gnl|CDD|153133 cd01583, IPMI, 3-isopropylmalate dehydratase catalyzes the
isomerization between 2-isopropylmalate and
3-isopropylmalate. Aconatase-like catalytic domain of
3-isopropylmalate dehydratase and related
uncharacterized proteins. 3-isopropylmalate dehydratase
catalyzes the isomerization between 2-isopropylmalate
and 3-isopropylmalate, via the formation of
2-isopropylmaleate 3-isopropylmalate. IPMI is involved
in fungal and bacterial leucine biosynthesis and is also
found in eukaryotes.
Length = 382
Score = 27.2 bits (61), Expect = 9.9
Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 11/60 (18%)
Query: 22 KAGYVPQDEVPLYESKGKQFANRQAAQSIP-------IGLDPS----HVKKPVNPQNPIP 70
KAG V DE KG+ A + +S + +D S V P +P N +P
Sbjct: 193 KAGIVAPDETTFEYLKGRGKAYWKELKSDEDAEYDKVVEIDASELEPQVAWPHSPDNVVP 252
>gnl|CDD|220710 pfam10351, Apt1, Golgi-body localisation protein domain. This is
the C-terminus of a family of proteins conserved from
plants to humans. The plant members are localised to the
Golgi proteins and appear to regulate membrane
trafficking, as they are required for rapid vesicle
accumulation at the tip of the pollen tube. The
C-terminus probably contains the Golgi localisation
signal and it is well-conserved.
Length = 451
Score = 27.3 bits (61), Expect = 9.9
Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 188 LNFDNLSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQLEKLQRKPDLLSEIMA 247
+ D E L+ R+ L++++RE+ + +++E E K +K+ L L E+
Sbjct: 85 FSSDFSDLEGLDSRVVALQERIRELAEIRRELEFRE-KLLDKEGWNDLL---LLEVELQR 140
Query: 248 LKLSLH 253
+ L L+
Sbjct: 141 VLLELY 146
>gnl|CDD|224658 COG1744, Med, Uncharacterized ABC-type transport system,
periplasmic component/surface lipoprotein [General
function prediction only].
Length = 345
Score = 27.3 bits (61), Expect = 10.0
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 10/42 (23%)
Query: 190 FDNLSPEELEKRIKNLKKKVREIKTLEQKIESGEIKNPEKDQ 231
PEE++K ++ L+ KI SGEI P K +
Sbjct: 308 LGKAVPEEVKK----------LVEALKAKIISGEITVPTKKE 339
>gnl|CDD|236255 PRK08385, PRK08385, nicotinate-nucleotide pyrophosphorylase;
Provisional.
Length = 278
Score = 27.0 bits (60), Expect = 10.0
Identities = 11/28 (39%), Positives = 20/28 (71%), Gaps = 1/28 (3%)
Query: 190 FDNLSPEELEKRIKNLKKK-VREIKTLE 216
DN++PEE+ + I+ LK++ +RE +E
Sbjct: 208 LDNMTPEEIREVIEALKREGLRERVKIE 235
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
0.310 0.133 0.376
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,298,690
Number of extensions: 1416897
Number of successful extensions: 3333
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3081
Number of HSP's successfully gapped: 361
Length of query: 267
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 172
Effective length of database: 6,723,972
Effective search space: 1156523184
Effective search space used: 1156523184
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 58 (26.2 bits)