RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy20
(147 letters)
>gnl|CDD|200948 pfam00038, Filament, Intermediate filament protein.
Length = 312
Score = 59.9 bits (146), Expect = 2e-11
Identities = 28/90 (31%), Positives = 50/90 (55%)
Query: 58 QEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDIR 117
EK +++NLNDRLA YI+ V+ L+ LE + + + + E ++ + E+EI ++R
Sbjct: 1 NEKEQMQNLNDRLASYIDKVRFLEQQNKELEAKIEELRQKKSAEPSRLYSLYEQEIRELR 60
Query: 118 KALDRESSSKSALAIEKRRLLDELLDLKNK 147
K LD ++ ++ L +E L D + K
Sbjct: 61 KQLDELTNERARLQLEIDNLRLAAEDFREK 90
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 33.0 bits (76), Expect = 0.046
Identities = 8/53 (15%), Positives = 16/53 (30%)
Query: 2 SGRSKRGATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLSPTII 54
+ A P+A+ +++ + P P P P P +
Sbjct: 399 PSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAG 451
>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 32.2 bits (73), Expect = 0.070
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 3 GRSKRGATPAKTPSASRGSSSRQTSEVREEPP-QPQPQSQPPRPGSPLSPTI 53
GA PA+ PS + + Q V P P PQ+ PR + P +
Sbjct: 410 KPEAPGARPAELPSPASAPTPEQQPPVARSAPLPPSPQASAPRNVASGKPGV 461
Score = 26.1 bits (57), Expect = 9.2
Identities = 10/56 (17%), Positives = 16/56 (28%)
Query: 9 ATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLSPTIISRRQEKNELK 64
A + + +E+ P P+ QPP S P +N
Sbjct: 401 QPDRHPGPAKPEAPGARPAELPSPASAPTPEQQPPVARSAPLPPSPQASAPRNVAS 456
>gnl|CDD|178697 PLN03152, PLN03152, hypothetical protein; Provisional.
Length = 241
Score = 31.0 bits (70), Expect = 0.16
Identities = 12/26 (46%), Positives = 13/26 (50%)
Query: 33 PPQPQPQSQPPRPGSPLSPTIISRRQ 58
P P PQ+ PR PLS SRR
Sbjct: 10 PHPPNPQNPNPRKPKPLSRCGASRRD 35
>gnl|CDD|202419 pfam02829, 3H, 3H domain. This domain is predicted to be a small
molecule binding domain, based on its occurrence with
other domains. The domain is named after its three
conserved histidine residues.
Length = 98
Score = 29.8 bits (68), Expect = 0.16
Identities = 12/47 (25%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 77 VQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDIRKALDRE 123
++KL++ KA L HT ++A E+ ++ I +AL ++
Sbjct: 53 MEKLESSKAKPLSELTGGVHLHT-----IEAPDEETLDKIEEALKKK 94
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 30.7 bits (69), Expect = 0.30
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 9 ATPAKTP--SASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLSP 51
A PA+ P +R + SR T P QP+ QP P P
Sbjct: 2876 AAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQ 2920
Score = 30.3 bits (68), Expect = 0.38
Identities = 12/51 (23%), Positives = 17/51 (33%), Gaps = 2/51 (3%)
Query: 4 RSKRGATPAK--TPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLSPT 52
R + AK P+ + + R P QP RP P +P
Sbjct: 2865 RPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPP 2915
Score = 29.5 bits (66), Expect = 0.77
Identities = 15/29 (51%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 25 QTSEVREEPPQPQPQ-SQPPRPGSPLSPT 52
Q PPQPQP PPRP PL+PT
Sbjct: 2918 QPQPQPPPPPQPQPPPPPPPRPQPPLAPT 2946
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 30.0 bits (68), Expect = 0.34
Identities = 8/49 (16%), Positives = 16/49 (32%), Gaps = 2/49 (4%)
Query: 4 RSKRGATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLSPT 52
R R ++R + + + +PP Q + P P +
Sbjct: 67 RVHRVNHAPANAQEH--EAARPSPQHQYQPPYASAQPRQPVQQPPEAQV 113
>gnl|CDD|222449 pfam13908, Shisa, Wnt and FGF inhibitory regulator. Shisa is a
transcription factor-type molecule that physically
interacts with immature forms of the Wnt receptor
Frizzled and the FGF receptor within the endoplasmic
reticulum to inhibit their post-translational maturation
and trafficking to the cell surface.
Length = 177
Score = 29.8 bits (67), Expect = 0.37
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 10/48 (20%)
Query: 14 TPSASRGSSSR-------QTSEVREEPPQPQPQ---SQPPRPGSPLSP 51
P +R +S+ Q P PQ Q PP+PG P P
Sbjct: 111 RPVMTRATSTTVQTTPLPQPPSTAPSYPGPQYQGYHPMPPQPGMPAPP 158
Score = 27.9 bits (62), Expect = 1.8
Identities = 12/35 (34%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 18 SRGSSSRQTSEVREEPPQPQPQSQPPR-PGSPLSP 51
R +R TS + P PQP S P PG
Sbjct: 110 QRPVMTRATSTTVQTTPLPQPPSTAPSYPGPQYQG 144
>gnl|CDD|227765 COG5478, COG5478, Predicted small integral membrane protein
[Function unknown].
Length = 141
Score = 29.3 bits (66), Expect = 0.48
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 76 LVQKLQN-D----KASLEYSLYSIEESHTTEFKKVKAASEKEIEDIRKALDRESSSKSAL 130
L+Q QN D +A L+ + S+ E+ + ++ +EIE+IR L+ E+ + +
Sbjct: 64 LIQNTQNRDTAAIQAKLDELIRSLREARN-DVVGIEHLKPEEIEEIRDRLEDEAGTGDGV 122
Query: 131 AI 132
Sbjct: 123 PT 124
>gnl|CDD|204032 pfam08703, PLC-beta_C, PLC-beta C terminal. This domain
corresponds to the alpha helical C terminal domain of
phospholipase C beta.
Length = 181
Score = 29.4 bits (66), Expect = 0.50
Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 58 QEKNELKNLNDRLAQY-IELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDI 116
+++ + + L R QY E +K Q+ K ++ E + KK+K SEKE +++
Sbjct: 9 KDRQQQELLELREEQYDSEKKRKEQHLKEQIQKLTELAREKQAAQLKKLKEISEKEKKEL 68
Query: 117 RKALDRESSSKSALAIEKRRLLDELL 142
+K LDR+ + A K + E
Sbjct: 69 KKKLDRKRLERIQEAKTKEKHAQERE 94
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 29.6 bits (67), Expect = 0.55
Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 16/80 (20%)
Query: 55 SRRQEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIE 114
+R+E+ E +N D LA E K DK E K EK +
Sbjct: 518 KKRKEEIEARNNADSLAYQAEKTLKEAGDKLPAE----------------EKEKIEKAVA 561
Query: 115 DIRKALDRESSSKSALAIEK 134
++++AL E + E+
Sbjct: 562 ELKEALKGEDVEEIKAKTEE 581
>gnl|CDD|217011 pfam02388, FemAB, FemAB family. The femAB operon codes for two
nearly identical approximately 50-kDa proteins involved
in the formation of the Staphylococcal pentaglycine
interpeptide bridge in peptidoglycan. These proteins are
also considered as a factor influencing the level of
methicillin resistance.
Length = 408
Score = 29.5 bits (67), Expect = 0.58
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 65 NLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHT----TEFKKVKAASEKEIEDIRKAL 120
N + L + E ++KL+ D A LE L S E ++ A+ EK I++ ++ +
Sbjct: 239 NFKEYLDELQEKLEKLEKDLAKLEEKLEKNPNSKKKNKLAELEQQLASLEKRIDEAKELI 298
Query: 121 D 121
Sbjct: 299 A 299
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.4 bits (67), Expect = 0.63
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 3/87 (3%)
Query: 57 RQEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDI 116
R+ +NEL+ L RL Q E + + E L E+ + ++++ E+E+E++
Sbjct: 78 RERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKK-EEELEEL 136
Query: 117 RKALDRESSSKSALAIE--KRRLLDEL 141
+ +E S L E K LL+++
Sbjct: 137 IEEQLQELERISGLTAEEAKEILLEKV 163
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 29.1 bits (65), Expect = 0.87
Identities = 7/40 (17%), Positives = 16/40 (40%)
Query: 9 ATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSP 48
+PA P+ + + + P P+++ P+ P
Sbjct: 22 PSPAAAPAPPPPAKTAAPATKAAAPAAAAPRAEKPKKDKP 61
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 28.9 bits (65), Expect = 1.2
Identities = 23/101 (22%), Positives = 41/101 (40%), Gaps = 14/101 (13%)
Query: 42 PPRPGSPLSPTIISR-----RQEKNEL------KNLNDRLAQYIELVQKLQNDKAS---L 87
PP P SP + + R++K E K + ++ + +E V K +A
Sbjct: 78 PPDPLSPGEQGLQRKLKELEREQKEEEVREKHNKKIIEKFGEDLEEVYKFMKGEAKVEEE 137
Query: 88 EYSLYSIEESHTTEFKKVKAASEKEIEDIRKALDRESSSKS 128
E I E + K+ K ++ + KAL +ES ++
Sbjct: 138 EEKQMEILEKALKSYLKIVKEENKSLQRLAKALQKESEERT 178
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 27.7 bits (62), Expect = 1.7
Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 15/102 (14%)
Query: 49 LSPTIISRRQ---EKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKV 105
LS T +R + + EL L + LA+ E + +LQ + L+ L ++E
Sbjct: 58 LSDTPSARERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAE-------- 109
Query: 106 KAASEKEIEDIRKALDRESSSKSALAIEKRRLLDELLDLKNK 147
+KE+ I++ S++ L E R L +EL +LK +
Sbjct: 110 LERLQKELARIKQL----SANAIELDEENRELREELAELKQE 147
>gnl|CDD|182904 PRK11020, PRK11020, hypothetical protein; Provisional.
Length = 118
Score = 27.3 bits (61), Expect = 1.9
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 14/70 (20%)
Query: 58 QEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHT--TEFKKVKAASEKEIED 115
EKNE+K L+DRL +++ A+ +F+K KA E EI
Sbjct: 2 VEKNEIKRLSDRL-------DAIRHKLAAASLR-----GDAEKYAQFEKEKATLEAEIAR 49
Query: 116 IRKALDRESS 125
+++ ++ S
Sbjct: 50 LKEVQSQKLS 59
>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 = 28.1 bits (63), Expect = 1.9
Identities = 26/96 (27%), Positives = 40/96 (41%), Gaps = 11/96 (11%)
Query: 59 EKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVK-------AASEK 111
E NELK DRL E +Q+L + A L ++ IE E ++ K E
Sbjct: 400 EINELKRELDRL---QEELQRLSEELADLNAAIAGIEAKIN-ELEEEKEDKALEIKKQEW 455
Query: 112 EIEDIRKALDRESSSKSALAIEKRRLLDELLDLKNK 147
++E + L + L E R+ EL L+ +
Sbjct: 456 KLEQLAADLSKYEQELYDLKEEYDRVEKELSKLQRE 491
Score = 27.7 bits (62), Expect = 2.4
Identities = 16/86 (18%), Positives = 37/86 (43%), Gaps = 1/86 (1%)
Query: 62 ELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDIRKALD 121
E++ R + E +L+ + L L +++ ++K +++E +++ ++
Sbjct: 344 EIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDY-REKLEKLKREIN 402
Query: 122 RESSSKSALAIEKRRLLDELLDLKNK 147
L E +RL +EL DL
Sbjct: 403 ELKRELDRLQEELQRLSEELADLNAA 428
>gnl|CDD|237560 PRK13922, PRK13922, rod shape-determining protein MreC;
Provisional.
Length = 276
Score = 27.6 bits (62), Expect = 2.0
Identities = 11/46 (23%), Positives = 21/46 (45%)
Query: 52 TIISRRQEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEES 97
++ R+E ELK L ++ +++L+ + A L L E
Sbjct: 70 SLFDLREENEELKKELLELESRLQELEQLEAENARLRELLNLKESL 115
>gnl|CDD|178347 PLN02746, PLN02746, hydroxymethylglutaryl-CoA lyase.
Length = 347
Score = 27.8 bits (62), Expect = 2.2
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 4/52 (7%)
Query: 89 YSLYSIEESHTTEFKKVKAASEKEIEDIRKALDRESSSKSALAIEKRRLLDE 140
Y L + S + K+ AA + I K L R S SK+A+A+ R
Sbjct: 297 YMLNGLGVSTNVDLGKLMAAGDF----ISKHLGRPSGSKTAVALSARITAAA 344
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 27.9 bits (62), Expect = 2.2
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 2/69 (2%)
Query: 56 RRQEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIE- 114
RR K + K L++ + + KL L YS ++ + TE K +K+ E
Sbjct: 331 RRVNKEDFKKLSEIQLRIVSQAWKLLEKGGILLYSTCTVTKEENTEVVKRFVYEQKDAEV 390
Query: 115 -DIRKALDR 122
DIR L+
Sbjct: 391 IDIRDKLEE 399
>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta;
Provisional.
Length = 464
Score = 28.0 bits (63), Expect = 2.3
Identities = 9/49 (18%), Positives = 15/49 (30%)
Query: 5 SKRGATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLSPTI 53
S GA PA A+ + + + ++ P P I
Sbjct: 85 SDAGAAPAAAAEAAAAAPAAAAAAAAKKAAPAPAAPAAPAAEVAADPDI 133
>gnl|CDD|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase;
Provisional.
Length = 418
Score = 27.7 bits (62), Expect = 2.3
Identities = 7/46 (15%), Positives = 13/46 (28%)
Query: 6 KRGATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLSP 51
A +A++ + P P + P P + P
Sbjct: 123 APPAAAPAAAAAAKAEKTTPEKPKAAAPTPEPPAASKPTPPAAAKP 168
>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 = 28.1 bits (63), Expect = 2.3
Identities = 21/91 (23%), Positives = 42/91 (46%), Gaps = 6/91 (6%)
Query: 60 KNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAAS------EKEI 113
+ EL LN+ A E ++ L+ A+ E L +EE + +++ + E+ I
Sbjct: 809 RAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELI 868
Query: 114 EDIRKALDRESSSKSALAIEKRRLLDELLDL 144
E++ L+ + +++L L EL +L
Sbjct: 869 EELESELEALLNERASLEEALALLRSELEEL 899
Score = 26.9 bits (60), Expect = 4.3
Identities = 20/88 (22%), Positives = 41/88 (46%), Gaps = 1/88 (1%)
Query: 60 KNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDIRKA 119
+ E++ L +++ + E + +L+ A L L +EE + +K ++I +RK
Sbjct: 676 RREIEELEEKIEELEEKIAELEKALAELRKELEELEEE-LEQLRKELEELSRQISALRKD 734
Query: 120 LDRESSSKSALAIEKRRLLDELLDLKNK 147
L R + L +L EL +L+ +
Sbjct: 735 LARLEAEVEQLEERIAQLSKELTELEAE 762
Score = 26.9 bits (60), Expect = 5.2
Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 1/90 (1%)
Query: 56 RRQEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIED 115
+ +++L L + LA+ E +++L+ + SLE L E+ E + E+++E
Sbjct: 325 LEELESKLDELAEELAELEEKLEELKEELESLEAEL-EELEAELEELESRLEELEEQLET 383
Query: 116 IRKALDRESSSKSALAIEKRRLLDELLDLK 145
+R + + ++L E RL L L+
Sbjct: 384 LRSKVAQLELQIASLNNEIERLEARLERLE 413
Score = 26.2 bits (58), Expect = 8.7
Identities = 21/87 (24%), Positives = 44/87 (50%), Gaps = 1/87 (1%)
Query: 61 NELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDIRKAL 120
L+ L + L + E +++ + + L L +EE E + + E+EIE+++K L
Sbjct: 232 LRLEELREELEELQEELKEAEEELEELTAELQELEEKLE-ELRLEVSELEEEIEELQKEL 290
Query: 121 DRESSSKSALAIEKRRLLDELLDLKNK 147
++ S L +K+ L + L +L+ +
Sbjct: 291 YALANEISRLEQQKQILRERLANLERQ 317
>gnl|CDD|178748 PLN03209, PLN03209, translocon at the inner envelope of chloroplast
subunit 62; Provisional.
Length = 576
Score = 28.0 bits (62), Expect = 2.3
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 5 SKRGATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRP----GSPLSP 51
S+R P K A+ G T V E P P + +PP+P PLSP
Sbjct: 325 SQR--VPPKESDAADGPKPVPTKPVTPEAPSPPIEEEPPQPKAVVPRPLSP 373
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 27.8 bits (62), Expect = 2.3
Identities = 16/52 (30%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 1 MSGRSKRGATPAKTPSASRGSSSRQTSEVREEPPQ-PQPQSQPPRPGSPLSP 51
S + +T A A GS + + PP P P S PP P LS
Sbjct: 85 RSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLSE 136
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 28.0 bits (63), Expect = 2.4
Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 10/84 (11%)
Query: 62 ELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDIRKALD 121
+L D+L Y+ + L+ +K + +++ E+E+E I K +
Sbjct: 54 KLSEALDKLRSYLPKLNPLREEKKKVSVK----------SLEELIKDVEEELEKIEKEIK 103
Query: 122 RESSSKSALAIEKRRLLDELLDLK 145
S L E + L E+ L+
Sbjct: 104 ELEEEISELENEIKELEQEIERLE 127
>gnl|CDD|184256 PRK13700, PRK13700, conjugal transfer protein TraD; Provisional.
Length = 732
Score = 28.0 bits (62), Expect = 2.4
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 3 GRSKRGATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLSPTI 53
GR P + G Q +E ++P QPQ QP +P P+SP I
Sbjct: 596 GRQMASLFEPDVPEVASGEDVTQ-AEQPQQPQQPQQPQQPQQPQQPVSPVI 645
>gnl|CDD|233734 TIGR02120, GspF, type II secretion system protein F. This membrane
protein is a component of the terminal branch complex of
the general secretion pathway (GSP), also known as
the"Type II" secretion pathway. The GSP transports
proteins (generally virulence-associated cell wall
hydrolases) across the outer membrase of the bacterial
cell. Transport across the inner membrane is often, but
not exclusively handled by the Sec system. This model
was constructed from the broader subfamily model,
pfam00482 which includes components of pilin complexes
(PilC) as well as other related genes. GspF is nearly
always gene clustered with other GSP subunits. Some
genes from Xylella and Xanthomonas strains score below
the trusted cutoff due to excessive divergence from the
family such that a sequence from Deinococcus which does
not appear to be GspF scores higher [Protein fate,
Protein and peptide secretion and trafficking].
Length = 399
Score = 27.3 bits (61), Expect = 2.9
Identities = 16/55 (29%), Positives = 25/55 (45%)
Query: 27 SEVREEPPQPQPQSQPPRPGSPLSPTIISRRQEKNELKNLNDRLAQYIELVQKLQ 81
S V E +Q PR PL +++ + L + +RLA Y+E Q L+
Sbjct: 105 SRVLEGKSLADALAQHPRDFPPLYRALVAAGEASGALDAVLERLADYLEERQALR 159
>gnl|CDD|234977 PRK01741, PRK01741, cell division protein ZipA; Provisional.
Length = 332
Score = 27.4 bits (61), Expect = 3.0
Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 3/68 (4%)
Query: 3 GRSKRGATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLSPTIISRRQEKNE 62
R++ + P A + ++ S V PP P QP S + +++ +
Sbjct: 41 TRTRPPSRPISNEEADQPNTLNPQSYVETTPP---PFQQPQTEESESENEVQIQQEVEQS 97
Query: 63 LKNLNDRL 70
+ + L
Sbjct: 98 VDEIKITL 105
>gnl|CDD|233360 TIGR01330, bisphos_HAL2, 3'(2'),5'-bisphosphate nucleotidase, HAL2
family. Sulfate is incorporated into
3-phosphoadenylylsulfate, PAPS, for utilization in
pathways such as methionine biosynthesis. Transfer of
sulfate from PAPS to an acceptor leaves adenosine
3'-5'-bisphosphate, APS. This model describes a form
found in plants of the enzyme 3'(2'),5'-bisphosphate
nucleotidase, which removes the 3'-phosphate from APS to
regenerate AMP and help drive the cycle. Sensitivity of
this essential enzyme to sodium and other metal ions
results is responsible for characterization of this
enzyme as a salt tolerance protein. Some members of this
family are active also as inositol 1-monophosphatase.
Length = 353
Score = 27.5 bits (61), Expect = 3.1
Identities = 6/30 (20%), Positives = 13/30 (43%)
Query: 96 ESHTTEFKKVKAASEKEIEDIRKALDRESS 125
+ +KK K +ED+ + +D +
Sbjct: 95 LVYAKNYKKDDQFPLKSLEDVLQIIDFGNY 124
>gnl|CDD|133445 cd01076, NAD_bind_1_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 1. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
assimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 227
Score = 27.1 bits (61), Expect = 3.4
Identities = 15/47 (31%), Positives = 19/47 (40%)
Query: 73 YIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDIRKA 119
Y E VQ LQ E +E F+ V +EK D+R A
Sbjct: 170 YFEWVQNLQGFYWDEEEVNSRLETKMREAFEAVLETAEKYGVDLRTA 216
>gnl|CDD|221480 pfam12238, MSA-2c, Merozoite surface antigen 2c. This family of
proteins is found in eukaryotes. Proteins in this family
are typically between 263 and 318 amino acids in length.
There is a conserved SFT sequence motif. MSA-2 is a
plasma membrane glycoprotein which can be found in
Babesia bovis species.
Length = 201
Score = 27.1 bits (60), Expect = 3.6
Identities = 11/39 (28%), Positives = 16/39 (41%)
Query: 10 TPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSP 48
PA+ S SS ++ + S PP PG+P
Sbjct: 137 APAEYYSPKHSSSQGTSTTRPSDGSATPNTSAPPTPGNP 175
>gnl|CDD|215656 pfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold
many proteins. Hsp70 assisted folding involves repeated
cycles of substrate binding and release. Hsp70 activity
is ATP dependent. Hsp70 proteins are made up of two
regions: the amino terminus is the ATPase domain and the
carboxyl terminus is the substrate binding region.
Length = 598
Score = 27.2 bits (61), Expect = 3.7
Identities = 23/98 (23%), Positives = 38/98 (38%), Gaps = 6/98 (6%)
Query: 39 QSQPPRPGSPLSPTIISRRQEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESH 98
Q S LS I R + E D + ++ K E +YS+E+S
Sbjct: 491 QKITITASSGLSDDEIERMVKDAEEYAAED------KKRKERIEAKNEAEEYVYSLEKSL 544
Query: 99 TTEFKKVKAASEKEIEDIRKALDRESSSKSALAIEKRR 136
E K+ A +K++E+ + L E + IE +
Sbjct: 545 KEEGDKLPEADKKKVEEAIEWLKEELEGEDKEEIEAKT 582
>gnl|CDD|185668 PTZ00490, PTZ00490, Ferredoxin superfamily; Provisional.
Length = 143
Score = 26.4 bits (58), Expect = 4.1
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 100 TEFKKVKAASEKEIEDIRKALDRESSSKSALAI 132
FKK+ SE+E + + KALD + +S+ A +
Sbjct: 90 ASFKKLGGPSEEEEDVLAKALDVKETSRLACQV 122
>gnl|CDD|171499 PRK12438, PRK12438, hypothetical protein; Provisional.
Length = 991
Score = 27.1 bits (60), Expect = 4.1
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 20 GSSSRQTSEVREEPPQPQPQSQPPRPGSPLSP 51
G+ T+ + P P + PP P + P
Sbjct: 898 GTGRVATAPGGDAASAPPPGAGPPAPPQAVPP 929
>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 = 26.8 bits (60), Expect = 4.5
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 3/87 (3%)
Query: 57 RQEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDI 116
++ +NEL+ L RL Q E + + E +L E+ + + K + E+E+E++
Sbjct: 72 KERRNELQRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLD-EKEEELEEL 130
Query: 117 RKALDRESSSKSALAIE--KRRLLDEL 141
E S L E K LL+E+
Sbjct: 131 IAEQREELERISGLTQEEAKEILLEEV 157
>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter. This
model describes the photoreceptor protein (rim protein)
in eukaryotes. It is the member of ABC transporter
superfamily. Rim protein is a membrane glycoprotein which
is localized in the photoreceptor outer segment discs.
Mutation/s in its genetic loci is implicated in the
recessive Stargardt's disease [Transport and binding
proteins, Other].
Length = 2272
Score = 27.3 bits (60), Expect = 4.6
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 8/47 (17%)
Query: 4 RSKRGATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLS 50
K G TP + + S G + P+ QP +P PG PL+
Sbjct: 1307 TEKAGQTPQASHTCSPGQPA--------AHPEGQPPPEPEDPGVPLN 1345
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 27.0 bits (60), Expect = 4.6
Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 2/86 (2%)
Query: 58 QEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASE--KEIED 115
+ K+EL+ L + L + E + +L+ + LE + + E +++ E +E+++
Sbjct: 271 ELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKE 330
Query: 116 IRKALDRESSSKSALAIEKRRLLDEL 141
+AL E + L E +LL EL
Sbjct: 331 KIEALKEELEERETLLEELEQLLAEL 356
>gnl|CDD|222579 pfam14179, YppG, YppG-like protein. The YppG-like protein family
includes the B. subtilis YppG protein, which is
functionally uncharacterized. This family of proteins
is found in bacteria. Proteins in this family are
typically between 115 and 181 amino acids in length.
There are two completely conserved residues (F and G)
that may be functionally important.
Length = 110
Score = 26.2 bits (58), Expect = 4.7
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 32 EPPQPQPQSQPPRPGSPLSP 51
P Q Q QPP+ S LS
Sbjct: 52 YPKQSPQQQQPPQFSSFLSQ 71
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 26.6 bits (59), Expect = 5.2
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 5/88 (5%)
Query: 56 RRQEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIED 115
+Q + E+ L ++ + + KL+ SLE + S+E E K+I D
Sbjct: 40 LKQIQKEIAALEKKIREQQDQRAKLEKQLKSLETEIASLEAQ-LIETADDLKKLRKQIAD 98
Query: 116 IRKALDRESSSKSALAIEKRRLLDELLD 143
+ L+ + E+RR L E L
Sbjct: 99 LNARLNALEVQE----REQRRRLAEQLA 122
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 26.8 bits (60), Expect = 5.5
Identities = 24/85 (28%), Positives = 35/85 (41%), Gaps = 16/85 (18%)
Query: 62 ELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDIRKALD 121
EL +L +L EL Q+L + + LE L E+ T A +E E++ + K L
Sbjct: 57 ELSSLKAKLDTLEELRQRLDDLEELLE--LAEEEDDEET-----LAEAEAELKALEKKLA 109
Query: 122 RESSSKSALAIEKRRLLDELLDLKN 146
+E RLL D N
Sbjct: 110 A---------LELERLLSGEYDANN 125
>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 = 26.1 bits (58), Expect = 5.5
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 61 NELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTT-EFKKVKAASEKEIEDIRKA 119
EL L+ + + E VQ L+ D ++LE L S+ TT E ++ +KE+ +I +
Sbjct: 72 EELNKLDMEIEELREEVQLLKQDCSTLEIELKSLTSDLTTEELQEEIQELKKEVREIEEK 131
Query: 120 LD 121
L+
Sbjct: 132 LE 133
>gnl|CDD|237963 PRK15424, PRK15424, propionate catabolism operon regulatory protein
PrpR; Provisional.
Length = 538
Score = 26.6 bits (59), Expect = 5.6
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 5/70 (7%)
Query: 62 ELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDIRKALD 121
EL+NL +RLA ++ + L+ L + A +++AL+
Sbjct: 453 ELRNLMERLALFLSVEPTPDLTPQFLQLLLPELARESAK-----TPAPRLLAATLQQALE 507
Query: 122 RESSSKSALA 131
R + K+A A
Sbjct: 508 RFNGDKTAAA 517
>gnl|CDD|149105 pfam07851, TMPIT, TMPIT-like protein. A number of members of this
family are annotated as being transmembrane proteins
induced by tumour necrosis factor alpha, but no
literature was found to support this.
Length = 330
Score = 26.6 bits (59), Expect = 6.1
Identities = 12/73 (16%), Positives = 26/73 (35%), Gaps = 7/73 (9%)
Query: 57 RQEKNELKNLNDRLAQYIEL---VQKLQNDKASL----EYSLYSIEESHTTEFKKVKAAS 109
++ + E + L + Y + V+KLQ S L + S K +
Sbjct: 7 KELEKEFQQLQETHRLYKQKLEEVEKLQEQCTSAIARQRKRLKQLIVSLKKLKKSLTPED 66
Query: 110 EKEIEDIRKALDR 122
+ +E + + +
Sbjct: 67 SELVEQLEEQIKE 79
>gnl|CDD|238872 cd01834, SGNH_hydrolase_like_2, SGNH_hydrolase subfamily. SGNH
hydrolases are a diverse family of lipases and
esterases. The tertiary fold of the enzyme is
substantially different from that of the alpha/beta
hydrolase family and unique among all known hydrolases;
its active site closely resembles the Ser-His-Asp(Glu)
triad found in other serine hydrolases.
Length = 191
Score = 26.1 bits (58), Expect = 6.2
Identities = 8/33 (24%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 49 LSPTIISR-RQEKNELKNLNDRLAQYIELVQKL 80
+SP + N LA Y + V++L
Sbjct: 110 VSPIAYEANEDPLPDGAEYNANLAAYADAVREL 142
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 26.7 bits (59), Expect = 6.4
Identities = 10/34 (29%), Positives = 15/34 (44%)
Query: 9 ATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQP 42
A + +A+ S S S +P PQ +QP
Sbjct: 387 AAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQP 420
>gnl|CDD|225499 COG2948, VirB10, Type IV secretory pathway, VirB10 components
[Intracellular trafficking and secretion].
Length = 360
Score = 26.3 bits (58), Expect = 6.6
Identities = 15/70 (21%), Positives = 25/70 (35%), Gaps = 9/70 (12%)
Query: 1 MSGRSKRGATPAKTPSASRGSSSRQTSEVREEPPQP-QPQSQPPRPGSPLSPTIISRRQE 59
+ G KR + RG+ PP P P PP P +P + ++ E
Sbjct: 46 LQGEKKRINNTQPPSNVERGTPP--------LPPLPDDPPLPPPLPVDLGAPVLPDQQVE 97
Query: 60 KNELKNLNDR 69
+ + + R
Sbjct: 98 EAKDQPRRLR 107
>gnl|CDD|220817 pfam10593, Z1, Z1 domain. This uncharacterized domain was
identified by Iyer and colleagues. It is found
associated with a helicase domain of superfamily type
II.
Length = 231
Score = 26.1 bits (58), Expect = 7.0
Identities = 20/88 (22%), Positives = 43/88 (48%), Gaps = 13/88 (14%)
Query: 54 ISRRQEKNELKNLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFK---------- 103
+SR + K + D + +Y+ ++K + L ++ ++E + +F+
Sbjct: 33 VSRFT--DVHKQVADLIEEYLNSLRKAVENGDDLGETIAELKELYEDDFEPGTDLDKPSW 90
Query: 104 -KVKAASEKEIEDIRKALDRESSSKSAL 130
+++AA K I+DIR + S+SK +L
Sbjct: 91 DEIQAALPKVIDDIRVVVVNSSTSKDSL 118
>gnl|CDD|165528 PHA03270, PHA03270, envelope glycoprotein C; Provisional.
Length = 466
Score = 26.4 bits (58), Expect = 7.2
Identities = 14/56 (25%), Positives = 19/56 (33%), Gaps = 9/56 (16%)
Query: 2 SGRSKRGATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLSPTIISRR 57
SG P TP+ +RG + P P + P SP +P R
Sbjct: 39 SGSPGSAEGPRTTPTPTRGKGT---------PTGPASPPKSGPPKSPPAPFRCKRP 85
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 26.4 bits (59), Expect = 7.6
Identities = 28/138 (20%), Positives = 44/138 (31%), Gaps = 21/138 (15%)
Query: 8 GATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLS--PTIISRRQEKNELK- 64
A +A + PQ P P S L + R Q + K
Sbjct: 381 AQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQLQRAQGATKAKK 440
Query: 65 -------------NLNDRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEK 111
+ +RLA L+ A E Y + ++ E KK A+ K
Sbjct: 441 SEPAAASRARPVNSALERLASVRPAPSALEKAPAKKEA--YRWKATNPVEVKKEPVATPK 498
Query: 112 EIEDIRKALDRESSSKSA 129
++KAL+ E + + A
Sbjct: 499 A---LKKALEHEKTPELA 513
>gnl|CDD|204792 pfam11947, DUF3464, Protein of unknown function (DUF3464). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 137 to
196 amino acids in length.
Length = 149
Score = 25.8 bits (57), Expect = 8.1
Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 1/57 (1%)
Query: 1 MSGRSKRGATPAKTPSASRGSSSRQTSEVREEPPQPQPQSQPPRPGSPLSPTIISRR 57
M+ KR K + R+ + + + Q +P+S+ S + P ++S R
Sbjct: 1 MASSRKRLPFEPKRSRKKGVKALRKAAVAKSKDKQKKPKSKRAASESGI-PKVVSNR 56
>gnl|CDD|236365 PRK09041, motB, flagellar motor protein MotB; Validated.
Length = 317
Score = 26.1 bits (58), Expect = 8.2
Identities = 20/78 (25%), Positives = 29/78 (37%), Gaps = 4/78 (5%)
Query: 10 TPAKTPSASRGSSSRQTSEVR---EEPPQPQPQSQPPRPGSPLSPTIISRRQEKNELKNL 66
TP K SS TS + ++ Q + +P R+E+ L+ L
Sbjct: 64 TPLKVALTGGDRSSDSTSPIPGGGDDITQQDGEVNK-QPNIAELAQGEKERREQERLEKL 122
Query: 67 NDRLAQYIELVQKLQNDK 84
L Q IE KL+ K
Sbjct: 123 KQELDQAIESNPKLRQFK 140
>gnl|CDD|239776 cd04243, AAK_AK-HSDH-like, AAK_AK-HSDH-like: Amino Acid Kinase
Superfamily (AAK), AK-HSDH-like; this family includes
the N-terminal catalytic domain of aspartokinase (AK) of
the bifunctional enzyme AK- homoserine dehydrogenase
(HSDH). These aspartokinases are found in such bacteria
as E. coli (AKI-HSDHI, ThrA and AKII-HSDHII, MetL) and
in higher plants (Z. mays AK-HSDH). AK and HSDH are the
first and third enzymes in the biosynthetic pathway of
the aspartate family of amino acids. AK catalyzes the
phosphorylation of Asp to P-aspartyl phosphate. HSDH
catalyzes the NADPH-dependent conversion of Asp
3-semialdehyde to homoserine. ThrA and MetL are involved
in threonine and methionine biosynthesis, respectively.
In E. coli, ThrA is subject to allosteric regulation by
the end product L-threonine and the native enzyme is
reported to be tetrameric. As with bacteria, plant AK
and HSDH are feedback inhibited by pathway end products.
Maize AK-HSDH is a Thr-sensitive 180-kD enzyme.
Arabidopsis AK-HSDH is an alanine-activated,
threonine-sensitive enzyme whose ACT domains, located
C-terminal to the AK catalytic domain, were shown to be
involved in allosteric activation. Also included in this
CD is the catalytic domain of the aspartokinase (AK) of
the lysine-sensitive aspartokinase isoenzyme AKIII, a
monofunctional class enzyme (LysC) found in some
bacteria such as E. coli. In E. coli, LysC is reported
to be a homodimer of 50 kD subunits. Also included in
this CD is the catalytic domain of aspartokinase (AK)
of the bifunctional enzyme AK - DAP decarboxylase
(DapDC) found in some bacteria. DapDC, which is the lysA
gene product, catalyzes the decarboxylation of DAP to
lysine.
Length = 293
Score = 26.0 bits (58), Expect = 8.4
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 19/77 (24%)
Query: 68 DRLAQYIELVQKLQNDKASLEYSLYSIEESHTTEFKKVKAASEKEIEDIRKALDRESSSK 127
+RL + L + + + L I E H ++ I++ L ES+++
Sbjct: 44 NRL---VALAELAASGDDAQAIVLQEIRERH--------------LDLIKELLSGESAAE 86
Query: 128 SALAIEKRRLLDELLDL 144
A++ LL+ L DL
Sbjct: 87 LLAALD--SLLERLKDL 101
>gnl|CDD|234528 TIGR04264, hyperosmo_Ebh, hyperosmolarity resistance protein Ebh,
N-terminal domain. Staphylococcal protein Ebh
(extracellular matrix-binding protein homolog) is a
giant protein, sometimes over 10,000 amino acids long as
reported. This model describes a non-repetitive
amino-terminal domain of about 2400 amino acids.
Length = 2354
Score = 26.3 bits (58), Expect = 8.4
Identities = 10/45 (22%), Positives = 18/45 (40%)
Query: 31 EEPPQPQPQSQPPRPGSPLSPTIISRRQEKNELKNLNDRLAQYIE 75
++PP + +P S + R N LK N ++ Y+
Sbjct: 840 DKPPIVLSNQEKIVVVNPTSISQDERNDIINALKAKNTNISSYLA 884
>gnl|CDD|216648 pfam01690, PLRV_ORF5, Potato leaf roll virus readthrough protein.
This family consists mainly of the potato leaf roll
virus readthrough protein. This is generated via a
readthrough of open reading frame 3 a coat protein
allowing transcription of open reading frame 5 to give
an extended coat protein with a large c-terminal
addition or read through domain. The readthrough
protein is thought to play a role in the circulative
aphid transmission of potato leaf roll virus. Also in
the family is open reading frame 6 from beet western
yellows virus and potato leaf roll virus both
luteovirus and an unknown protein from cucurbit
aphid-borne yellows virus a closterovirus.
Length = 460
Score = 25.8 bits (57), Expect = 9.3
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 11/52 (21%)
Query: 33 PPQPQPQSQPPRP-------GSPLSPTIISRRQEKN--ELKNLNDRLAQYIE 75
PP P P+ P + G+P T IS R+ + ++ L D+ +YIE
Sbjct: 17 PPAPTPEPTPAKHERFIGYVGTPQ--TKISTRENSDSISVRPLGDQRMRYIE 66
>gnl|CDD|114855 pfam06160, EzrA, Septation ring formation regulator, EzrA. During
the bacterial cell cycle, the tubulin-like cell-division
protein FtsZ polymerises into a ring structure that
establishes the location of the nascent division site.
EzrA modulates the frequency and position of FtsZ ring
formation.
Length = 559
Score = 26.0 bits (58), Expect = 9.4
Identities = 18/95 (18%), Positives = 41/95 (43%), Gaps = 8/95 (8%)
Query: 60 KNELKNLNDRLAQYIELVQKLQNDKASLE-------YSLYSIEESHTTEFKKVKAASEKE 112
K ++ D+L ++E ++ QN + LE Y+L E E +K E +
Sbjct: 301 KKFVEKNIDKLTDFLEHARE-QNKQLLLELDRLQQSYTLNEDELETVRELEKQLEELEAQ 359
Query: 113 IEDIRKALDRESSSKSALAIEKRRLLDELLDLKNK 147
+ + + + + + S L E + +L +++ +
Sbjct: 360 YDQLVERIAEKKVAYSELQEELEEIEKQLEEIEKE 394
>gnl|CDD|177878 PLN02234, PLN02234, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 641
Score = 25.8 bits (56), Expect = 9.8
Identities = 19/53 (35%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 22 SSRQTSEVREEPPQPQPQSQPPRPGSPLSPTIISRRQEKN----ELKNLNDRL 70
SS + S+VR + + RP +PL TI KN ELK L+D L
Sbjct: 39 SSTKYSKVRATTFSEKGEYYSNRPPTPLLDTINHPMHMKNLSIKELKVLSDEL 91
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
0.303 0.121 0.314
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: 7,198,364
Number of extensions: 633201
Number of successful extensions: 1737
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1606
Number of HSP's successfully gapped: 358
Length of query: 147
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 59
Effective length of database: 7,034,450
Effective search space: 415032550
Effective search space used: 415032550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 54 (24.7 bits)