RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780218|ref|YP_003064631.1| thymidylate kinase [Candidatus
Liberibacter asiaticus str. psy62]
(225 letters)
>gnl|CDD|30474 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 194 bits (495), Expect = 2e-50
Identities = 86/205 (41%), Positives = 130/205 (63%), Gaps = 6/205 (2%)
Query: 4 GLFISFEGIEGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPAAEAARHVLLSCGVDEFG 63
G+FI EGI+GAGKTT LLK L+ + V +TREPGGTP E R +LL+ G ++
Sbjct: 3 GMFIVIEGIDGAGKTTQAELLKERLEERGIKVVLTREPGGTPIGEKIRELLLN-GEEKLS 61
Query: 64 AEAEAIVFAAARLDHVENVIRPALMEGKILLCDRFLDSSYAYQGERDSSQHLFLDSLQEI 123
+AEA++FAA R H+E VI+PAL EGK+++CDR++DSS AYQG ++ +L E
Sbjct: 62 PKAEALLFAADRAQHLEEVIKPALKEGKVVICDRYVDSSLAYQGGGRGLDLDWVLALNEF 121
Query: 124 SVQEVMPDCTIILDLPVDIGLKRVQNRYSLRESACLDYFERKDVMIHEKRRQIFLDIARN 183
+ + PD T+ LD+P ++ L+R++ R LR D FE++D EK R+ +L++A
Sbjct: 122 APGGLKPDLTLYLDVPPEVALERIRKRGELR-----DRFEKEDDEFLEKVREGYLELAAK 176
Query: 184 QPDRCHIVDSAHSFQSVATNILNIV 208
P+R ++D++ + V IL I+
Sbjct: 177 FPERIIVIDASRPLEEVHEEILKIL 201
>gnl|CDD|30190 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known as
thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de novo
or salvage biosynthesis of thymidine triphosphate
(TTP)..
Length = 200
Score = 192 bits (488), Expect = 9e-50
Identities = 82/204 (40%), Positives = 125/204 (61%), Gaps = 6/204 (2%)
Query: 5 LFISFEGIEGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPAAEAARHVLLSCGVDEFGA 64
+FI FEGI+GAGKTT I LL L+ + Y+V +TREPGGTP EA R +LL ++
Sbjct: 1 MFIVFEGIDGAGKTTLIELLAERLEARGYEVVLTREPGGTPIGEAIRELLLDPEDEKMDP 60
Query: 65 EAEAIVFAAARLDHVENVIRPALMEGKILLCDRFLDSSYAYQGERDSSQHLFLDSLQEIS 124
AE ++FAA R HVE VI+PAL GKI+L DRF+DSS AYQG +++L +++
Sbjct: 61 RAELLLFAADRAQHVEEVIKPALARGKIVLSDRFVDSSLAYQGAGRGLGEALIEALNDLA 120
Query: 125 VQEVMPDCTIILDLPVDIGLKRVQNRYSLRESACLDYFERKDVMIHEKRRQIFLDIARNQ 184
+ PD TI+LD+ ++GL R++ R E++ + HE+ R+ +L++A +
Sbjct: 121 TGGLKPDLTILLDIDPEVGLARIEARGRDDR------DEQEGLEFHERVREGYLELAAQE 174
Query: 185 PDRCHIVDSAHSFQSVATNILNIV 208
P+R ++D++ + V IL +
Sbjct: 175 PERIIVIDASQPLEEVLAEILKAI 198
>gnl|CDD|145402 pfam02223, Thymidylate_kin, Thymidylate kinase.
Length = 186
Score = 151 bits (383), Expect = 2e-37
Identities = 75/196 (38%), Positives = 111/196 (56%), Gaps = 10/196 (5%)
Query: 9 FEGIEGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPAAEAARHVLLSCGVDEFGAEAEA 68
EG++GAGKTT LLK L+ + V +TREPGGTP E R +LL EA
Sbjct: 1 IEGLDGAGKTTQAELLKERLKEQGIKVVLTREPGGTPIGEKIRELLLRNEELSP--LTEA 58
Query: 69 IVFAAARLDHVENVIRPALMEGKILLCDRFLDSSYAYQGERDSSQHLFLDSLQEISVQEV 128
++FAA R++H+E I+PAL +GK ++CDR+L SS AYQG + SL V
Sbjct: 59 LLFAADRIEHLEEKIKPALKQGKTVICDRYLFSSIAYQGAAGGLGLDLVLSLNP-DVPGP 117
Query: 129 MPDCTIILDLPVDIGLKRVQNRYSLRESACLDYFERKDVMIHEKRRQIFLDIARNQPDRC 188
PD T +LD+ ++ LKR++ R L E FE + + K R+ +L++A+ +R
Sbjct: 118 KPDLTFLLDVDPEVALKRLRRRGELDE------FEFEQLDFLRKVRERYLELAK-DDERI 170
Query: 189 HIVDSAHSFQSVATNI 204
I+D+++S + V I
Sbjct: 171 LIIDASNSIEEVHEEI 186
>gnl|CDD|38537 KOG3327, KOG3327, KOG3327, Thymidylate kinase/adenylate kinase
[Nucleotide transport and metabolism].
Length = 208
Score = 51.5 bits (123), Expect = 2e-07
Identities = 53/221 (23%), Positives = 85/221 (38%), Gaps = 42/221 (19%)
Query: 1 MNSGLFISFEGIEGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPA-AEAARHVLLSCG- 58
M G I EG++ +GK+T L L PG PA S G
Sbjct: 2 MIRGALIVLEGLDRSGKSTQCGKLVESLI-----------PGLDPAELLRFPERSTSIGK 50
Query: 59 ------VDEFGAEAEAI--VFAAARLDHVENVIRPALMEGKILLCDRFLDSSYAYQGERD 110
+ I +F+A R +HV ++I+ L +G L+ DR+ S AY
Sbjct: 51 LIDGYLRKKSDLPDHTIHLLFSANRWEHV-SLIKEKLAKGTTLIVDRYSFSGVAYSA--- 106
Query: 111 SSQHLFLDSLQEISVQEVMPDCTIILDLPVDIGLKRVQ---NRYSLRESACLDYFERKDV 167
++ L LD ++ V PD + LD+ + +R RY + V
Sbjct: 107 -AKGLDLDWCKQPDVGLPKPDLVLFLDVSPEDAARRGGFGEERY-------------ETV 152
Query: 168 MIHEKRRQIFLDIARNQPDRCHIVDSAHSFQSVATNILNIV 208
EK F + R + H+VD++ S + V + ++V
Sbjct: 153 AFQEKVLVFFQKLLRKEDLNWHVVDASKSVEKVHQQVRSLV 193
>gnl|CDD|30191 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the
phosphorylation of deoxyribonucleosides to yield
corresponding monophosphates (dNMPs). This family
consists of various deoxynucleoside kinases including
deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC
2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC
2.7.1.21) kinases. They are key enzymes in the salvage
of deoxyribonucleosides originating from extra- or
intracellular breakdown of DNA..
Length = 193
Score = 36.4 bits (84), Expect = 0.007
Identities = 42/187 (22%), Positives = 69/187 (36%), Gaps = 21/187 (11%)
Query: 6 FISFEGIEGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPAAEAARHVLLSCGVDEFGAE 65
I EG GAGK+T L K + Y V EP + L ++
Sbjct: 1 VIVVEGNIGAGKST---LAKELAEHLGY--EVVPEPVEPDVEG---NPFLEKFYEDPKRW 52
Query: 66 AEA--IVFAAARLDHVENVI------RPALMEGKILLCDRFLDSSYAYQGERDSSQHLFL 117
A + F +RL ++ + + ++E I F +++ G + L+
Sbjct: 53 AFPFQLYFLLSRLKQYKDALEHLSTGQGVILERSIFSDRVFAEANLKEGGIMKTEYDLYN 112
Query: 118 DSLQEISVQEVMPDCTIILDLPVDIGLKRVQNRYSLRESAC-LDYFERKDVMIHEKRRQI 176
+ + + + PD I LD + LKR++ R E LDY E +HE +
Sbjct: 113 ELFDNLIPELLPPDLVIYLDASPETCLKRIKKRGRPEEQGIPLDYLED----LHEAYEKW 168
Query: 177 FLDIARN 183
FL
Sbjct: 169 FLPQMYE 175
>gnl|CDD|48379 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the
membrane by an interaction between SRP and its cognated
receptor (SR). In mammals, SRP consists of six protein
subunits and a 7SL RNA. One of these subunits is a 54
kd protein (SRP54), which is a GTP-binding protein that
interacts with the signal sequence when it emerges from
the ribosome. SRP54 is a multidomain protein that
consists of an N-terminal domain, followed by a central
G (GTPase) domain and a C-terminal M domain..
Length = 173
Score = 35.5 bits (82), Expect = 0.013
Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 14/88 (15%)
Query: 7 ISFEGIEGAGKTTHISLLKRFLQRKNYDVHV----TREPGGTPAAEAARHVLLSCGVDEF 62
I G++G GKTT + L +L++K V + T P A E R + GV F
Sbjct: 3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPA---AIEQLRVLGEQVGVPVF 59
Query: 63 ----GAEAEAIVFAA---ARLDHVENVI 83
G + +I A AR ++ + VI
Sbjct: 60 EEGEGKDPVSIAKRAIEHAREENFDVVI 87
>gnl|CDD|30887 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 34.7 bits (80), Expect = 0.019
Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 14/88 (15%)
Query: 7 ISFEGIEGAGKTTHISLLKRFLQRKNYDVHV----TREPGGTPAAEAARHVLLSCGVDEF 62
I G++G+GKTT L ++L++K V + T P A E + + GV F
Sbjct: 103 ILMVGLQGSGKTTTAGKLAKYLKKKGKKVLLVAADTYRPA---AIEQLKQLAEQVGVPFF 159
Query: 63 GAEAEA----IVFAA---ARLDHVENVI 83
G+ E I AA A+ + + VI
Sbjct: 160 GSGTEKDPVEIAKAALEKAKEEGYDVVI 187
>gnl|CDD|144151 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 32.1 bits (74), Expect = 0.14
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 7 ISFEGIEGAGKTTHISLLKRFLQRKNYDV 35
I G++G+GKTT I+ L +L+++ V
Sbjct: 4 ILLVGLQGSGKTTTIAKLAAYLKKQGKKV 32
>gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 31.8 bits (72), Expect = 0.17
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 7 ISFEGIEGAGKTTHISLLKRFLQRKNYDV 35
I F G+ G GKTT I+ L ++L+++ V
Sbjct: 142 ILFVGVNGVGKTTTIAKLAKYLKQQGKSV 170
>gnl|CDD|35999 KOG0780, KOG0780, KOG0780, Signal recognition particle, subunit
Srp54 [Intracellular trafficking, secretion, and
vesicular transport].
Length = 483
Score = 31.4 bits (71), Expect = 0.21
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 7 ISFEGIEGAGKTTHISLLKRFLQRKNYDV 35
I F G++G+GKTT + L + ++K Y V
Sbjct: 104 IMFVGLQGSGKTTTCTKLAYYYKKKGYKV 132
>gnl|CDD|39383 KOG4181, KOG4181, KOG4181, Uncharacterized conserved protein
[Function unknown].
Length = 491
Score = 30.9 bits (69), Expect = 0.33
Identities = 37/196 (18%), Positives = 66/196 (33%), Gaps = 21/196 (10%)
Query: 5 LFISFEGIEGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPAAEAARHVLLSCGVDEFGA 64
I G +G+GK+T +SLL +Y +V R P A E + +D
Sbjct: 189 TVIGVLGGQGSGKSTLLSLLAANSLDYDYRQYVFR-PVSPEADECIFAQ--THKIDPNIG 245
Query: 65 EAEAIVFAAAR-------LDHVENVIRPALMEGKILLCDRFLDSSYAYQGERDSSQHLFL 117
+ ++I+F + + + P LM DS + + L
Sbjct: 246 Q-KSILFLDTQPLQSFSIRERHILLDTPPLMPVG-------KDSDHQDLYSLGTMAFLLS 297
Query: 118 DSLQEISVQEVMPDCTIILDLPVDIGLKRVQNRYSLRESACLDYFERKDVMIHEKRRQIF 177
I V + + D +I L L+ + + D+ + V + K +I
Sbjct: 298 VCHIVIVVIDGLADEQLIRLLNAAERLRPTLAIFRHCKGYVRDHMPQL-VFVRAKAHRI- 355
Query: 178 LDIARNQPDRCHIVDS 193
D Q +R +
Sbjct: 356 -DFEPRQRERLDKKLA 370
>gnl|CDD|73013 cd03254, ABCC_Glucan_exporter_like, Glucan exporter ATP-binding
protein. In A. tumefaciens cyclic beta-1, 2-glucan
must be transported into the periplasmic space to exert
its action as a virluence factor. This subfamily
belongs to the MRP-like family and is involved in drug,
peptide, and lipid export. The MRP-like family,
similar to all ABC proteins, have a common four-domain
core structure constituted by two membrane-spanning
domains each composed of six transmembrane (TM) helices
and two nucleotide-binding domains (NBD). ABC
transporters are a subset of nucleotide hydrolases that
contain a signature motif, Q-loop, and H-loop/switch
region, in addition to, the Walker A motif/P-loop and
Walker B motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins..
Length = 229
Score = 30.2 bits (68), Expect = 0.48
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 2 NSGLFISFEGIEGAGKTTHISLLKRFLQ 29
G ++ G GAGKTT I+LL RF
Sbjct: 27 KPGETVAIVGPTGAGKTTLINLLMRFYD 54
>gnl|CDD|31833 COG1647, COG1647, Esterase/lipase [General function prediction
only].
Length = 243
Score = 30.2 bits (68), Expect = 0.50
Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 6/56 (10%)
Query: 15 AGKTTHISLLKRFLQRKNYDVHVTREPG-GTPAAEAARHVLLSCGVDEFGAEAEAI 69
G + +L R+L Y V+ R PG GT + L ++ + E
Sbjct: 25 TGTPRDVRMLGRYLNENGYTVYAPRYPGHGTLPED-----FLKTTPRDWWEDVEDG 75
>gnl|CDD|73008 cd03249, ABC_MTABC3_MDL1_MDL2, MTABC3 (also known as ABCB6) is a
mitochondrial ATP-binding cassette protein involved in
iron homeostasis and one of four ABC transporters
expressed in the mitochondrial inner membrane, the
other three being MDL1(ABC7), MDL2, and ATM1. In fact,
the yeast MDL1 (multidrug resistance-like protein 1)
and MDL2 (multidrug resistance-like protein 2)
transporters are also included in this CD. MDL1 is an
ATP-dependent permease that acts as a high-copy
suppressor of ATM1 and is thought to have a role in
resistance to oxidative stress. Interestingly,
subfamily B is more closely related to the
carboxyl-terminal component of subfamily C than the two
halves of ABCC molecules are with one another..
Length = 238
Score = 29.7 bits (67), Expect = 0.60
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 1 MNSGLFISFEGIEGAGKTTHISLLKRF 27
+ G ++ G G GK+T +SLL+RF
Sbjct: 26 IPPGKTVALVGSSGCGKSTVVSLLERF 52
>gnl|CDD|80342 cd02120, PA_subtilisin_like, PA_subtilisin_like:
Protease-associated domain containing subtilisin-like
proteases. This group contains various PA
domain-containing subtilisin-like proteases including
melon cucumisin, Arabidopsis thaliana Ara12, a nodule
specific serine protease from Alnus glutinosa ag12,
members of the tomato P69 family, and tomato LeSBT2.
These proteins belong to the peptidase S8 family.
Cucumisin from the juice of melon fruits is a
thermostable serine peptidase, with a broad substrate
specificity for oligopeptides and proteins. A. thaliana
Ara12 is a thermostable, extracellular serine protease,
found chiefly in silique tissue and stem tissue. Ara12
is stimulated by Ca2+ ions. A. glutinosa ag12 is
expressed at high levels in the nodules, and at low
levels in the shoot tips; it is implicated in both
symbiotic and non-symbiotic processes in plant
development. The tomato P69 protease family is comprised
of various protein isoforms of approximately 69KDa.
These isoforms accumulate extracellularly. Some of the
P69 genes are tightly regulated in a tissue specific
fashion, and by environmental and developmental signals.
For example: infection with avirulent bacteria activates
transcription of the genes for the P69 B and C isoforms,
the P69 E transcript was detected only in roots, and the
P69F transcript only in hydathodes. The Tomato LeSBT2
subtilase transcript was not detected in flowers and
roots, but was present in cotyledons and leaves. The
significance of the PA domain to these proteins has not
been ascertained. It may be a protein-protein
interaction domain. At peptidase active sites, the PA
domain may participate in substrate binding and/or
promoting conformational changes, which influence the
stability and accessibility of the site to substrate..
Length = 126
Score = 28.9 bits (64), Expect = 1.1
Identities = 10/24 (41%), Positives = 18/24 (75%)
Query: 85 PALMEGKILLCDRFLDSSYAYQGE 108
P+ ++GKI+LCDR ++S +G+
Sbjct: 47 PSKVKGKIVLCDRGGNTSRVAKGD 70
>gnl|CDD|72905 cd04669, Nudix_Hydrolase_11, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent
cation, such as Mg2+ or Mn2+, for their activity and
contain a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability,
thereby serving as surveillance & "house-cleaning"
enzymes. Substrate specificity is used to define
families within the superfamily. Differences in
substrate specificity are determined by the N-terminal
extension or by residues in variable loop regions.
Mechanistically, substrate hydrolysis occurs by a
nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required..
Length = 121
Score = 28.7 bits (64), Expect = 1.2
Identities = 20/62 (32%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 20 HISLLKRFLQRKNYDVHV--TREPGGTPAAEAARHVLLSCGVDEFGAEAEAIVFAAARLD 77
I L++R K Y V E G TP A R L G+D E IV R +
Sbjct: 13 EILLIRRIKPGKTYYVFPGGGIEEGETPEEAAKREALEELGLDVRVEEIFLIVNQNGRTE 72
Query: 78 HV 79
H
Sbjct: 73 HY 74
>gnl|CDD|35278 KOG0055, KOG0055, KOG0055, Multidrug/pheromone exporter, ABC
superfamily [Secondary metabolites biosynthesis,
transport and catabolism].
Length = 1228
Score = 29.0 bits (65), Expect = 1.2
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 1 MNSGLFISFEGIEGAGKTTHISLLKRF 27
+ +G ++ G G+GK+T ISLL+RF
Sbjct: 1013 IRAGQTVALVGPSGSGKSTVISLLERF 1039
Score = 27.9 bits (62), Expect = 2.2
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 2 NSGLFISFEGIEGAGKTTHISLLKRF 27
SG ++ G G+GK+T I LL RF
Sbjct: 377 PSGQTVALVGPSGSGKSTLIQLLARF 402
>gnl|CDD|33963 COG4240, COG4240, Predicted kinase [General function prediction
only].
Length = 300
Score = 28.4 bits (63), Expect = 1.5
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 5 LFISFEGIEGAGKTTHISLLKRFLQRKN 32
L + G +G+GK+T +L+ R L K
Sbjct: 51 LIVGISGPQGSGKSTLSALIVRLLAAKG 78
>gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible
oxidation of CO to CO2. CODH contains a
nickel-iron-sulfur cluster (C-center) and an
iron-sulfur cluster (B-center). CO oxidation occurs at
the C-center. Three accessory proteins encoded by
cooCTJ genes are involved in nickel incorporation into
a nickel site. CooC functions as a nickel insertase
that mobilizes nickel to apoCODH using energy released
from ATP hydrolysis. CooC is a homodimer and has NTPase
activities. Mutation at the P-loop abolishs its
function..
Length = 116
Score = 28.6 bits (64), Expect = 1.6
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 7 ISFEGIEGAGKTTHISLLKRFLQRKNYDV 35
I+ G G GKTT +LL R+L K V
Sbjct: 2 IAITGKGGVGKTTIAALLARYLAEKGKPV 30
>gnl|CDD|31327 COG1132, MdlB, ABC-type multidrug transport system, ATPase and
permease components [Defense mechanisms].
Length = 567
Score = 28.1 bits (62), Expect = 1.9
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 1 MNSGLFISFEGIEGAGKTTHISLLKRFLQ 29
+ G ++ G G+GK+T I LL R
Sbjct: 352 IEPGEKVAIVGPSGSGKSTLIKLLLRLYD 380
>gnl|CDD|32268 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 28.0 bits (62), Expect = 2.2
Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 6/88 (6%)
Query: 11 GIEGAGKTTHISLLKRFLQRKNYDVHV--TREPGGTPAAEAARHVLLSCGVDEFGAEAEA 68
I G G S L L + ++V + +R P AA AA L++ G +E A
Sbjct: 5 AIIGTGNIG--SALALRLAKAGHEVIIGSSRGPKALAAAAAALGPLITGGSNEDAAALAD 62
Query: 69 IVFAAARLDHVENVIRP--ALMEGKILL 94
+V A + + +V+ + GKI++
Sbjct: 63 VVVLAVPFEAIPDVLAELRDALGGKIVI 90
>gnl|CDD|39379 KOG4177, KOG4177, KOG4177, Ankyrin [Cell wall/membrane/envelope
biogenesis].
Length = 1143
Score = 27.6 bits (61), Expect = 2.7
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 10/72 (13%)
Query: 20 HISLLKRFLQRKNYDVHVTREPGGTPAAEAARH-------VLLSCG--VDEFGAEAEAIV 70
++ L+K L+ DV+ + G TP +AA+ +LL G V+ + +
Sbjct: 552 NVDLVKFLLEHG-ADVNAKDKLGYTPLHQAAQQGHNDIAELLLKHGASVNAADLDGFTPL 610
Query: 71 FAAARLDHVENV 82
A RL ++ V
Sbjct: 611 HIAVRLGYLSVV 622
>gnl|CDD|30875 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 27.5 bits (61), Expect = 3.1
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 1 MNSGLFISFEGIEGAGKTTHISLLKRFLQRKNYDVHV 37
G I F G+ G+GK+T + L+ L K Y V++
Sbjct: 20 GQKGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYL 56
>gnl|CDD|36394 KOG1179, KOG1179, KOG1179, Very long-chain acyl-CoA
synthetase/fatty acid transporter [Lipid transport and
metabolism].
Length = 649
Score = 27.6 bits (61), Expect = 3.1
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 138 LPVDIGLKRVQNRYSLRESACLDYFERKDVMIHEKRRQ------IFLDIARNQPDRCHIV 191
L GL+ + Y R+ L + + I RR+ +FL R QPD+ I+
Sbjct: 38 LGWLFGLRALATPYLPRDLWGLLKYILVKIFIRGSRRERRTIAELFLSQVRRQPDKPAII 97
Query: 192 D 192
Sbjct: 98 Y 98
>gnl|CDD|30543 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 27.4 bits (61), Expect = 3.3
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 1 MNSGLFISFEGIEGAGKTTHISLLKRFLQRKNYDV---HVTREP 41
M+ GL I G G GK+T L+K L+ TR+P
Sbjct: 1 MSKGLLIVLSGPSGVGKST---LVKALLEDDKLRFSVSATTRKP 41
>gnl|CDD|33889 COG4133, CcmA, ABC-type transport system involved in cytochrome c
biogenesis, ATPase component [Posttranslational
modification, protein turnover, chaperones].
Length = 209
Score = 27.2 bits (60), Expect = 4.0
Identities = 15/54 (27%), Positives = 25/54 (46%)
Query: 1 MNSGLFISFEGIEGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPAAEAARHVL 54
+N+G + G GAGKTT + +L L+ +V+ EP + +L
Sbjct: 25 LNAGEALQITGPNGAGKTTLLRILAGLLRPDAGEVYWQGEPIQNVRESYHQALL 78
>gnl|CDD|31301 COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase
and related enzymes [Amino acid transport and
metabolism].
Length = 386
Score = 27.1 bits (60), Expect = 4.1
Identities = 18/80 (22%), Positives = 29/80 (36%), Gaps = 10/80 (12%)
Query: 5 LFISFEGIEGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPAAEAARHVLLSCGVDEFGA 64
L SF G+EG + L + V+ + + HVL + G+ E A
Sbjct: 297 LNFSFPGVEGESLLLALDL---------AGIAVSTGSACSSGSLEPSHVLRAMGISEELA 347
Query: 65 EAEAIVFAAARLDHVENVIR 84
+I F+ R E +
Sbjct: 348 HG-SIRFSLGRFTTEEEIDA 366
>gnl|CDD|34235 COG4604, CeuD, ABC-type enterochelin transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 252
Score = 27.1 bits (60), Expect = 4.2
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 3 SGLFISFEGIEGAGKTTHISLLKRFLQRKNYDVHVT-REPGGTPAAEAAR 51
G S G GAGK+T +S++ R L++ + ++ + E TP+ E A+
Sbjct: 26 KGGITSIIGPNGAGKSTLLSMMSRLLKKDSGEITIDGLELTSTPSKELAK 75
>gnl|CDD|35281 KOG0058, KOG0058, KOG0058, Peptide exporter, ABC superfamily
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 716
Score = 26.8 bits (59), Expect = 4.5
Identities = 22/91 (24%), Positives = 34/91 (37%), Gaps = 20/91 (21%)
Query: 11 GIEGAGKTTHISLLKRFLQR------------KNYDVHVTREPGGTPAAEAARHVLLSCG 58
G G+GK+T SLL RF + + R G E VL S
Sbjct: 501 GPSGSGKSTIASLLLRFYDPTSGRILLDGVPISDINHKYLRRKIGLVGQEP---VLFSGS 557
Query: 59 VDE---FGAEA--EAIVFAAARLDHVENVIR 84
+ E +G + + + AAA++ + I
Sbjct: 558 IRENIAYGLDNATDEEIEAAAKMANAHEFIT 588
>gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety
of proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion..
Length = 99
Score = 27.0 bits (59), Expect = 4.6
Identities = 18/82 (21%), Positives = 27/82 (32%), Gaps = 12/82 (14%)
Query: 7 ISFEGIEGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPAAEAARHVLLSCGVDEFGAEA 66
I G G GKTT + L L ++ V + + +VL+ G
Sbjct: 2 IVVTGKGGVGKTTLAANLAAALAKRGKRVLLIDD-----------YVLIDTPPG-LGLLV 49
Query: 67 EAIVFAAARLDHVENVIRPALM 88
+ A D V V P +
Sbjct: 50 LLCLLALLAADLVIIVTTPEAL 71
>gnl|CDD|72973 cd03214, ABC_Iron-Siderophores_B12_Hemin, ABC transporters,
involved in the uptake of siderophores, heme, and
vitamin B12, are widely conserved in bacteria and
archaea. Only very few species lack representatives of
the siderophore family transporters. The E. coli BtuCD
protein is an ABC transporter mediating vitamin B12
uptake. The two ATP-binding cassettes (BtuD) are in
close contact with each other, as are the two
membrane-spanning subunits (BtuC); this arrangement is
distinct from that observed for the E. coli lipid
flippase MsbA. The BtuC subunits provide 20
transmembrane helices grouped around a translocation
pathway that is closed to the cytoplasm by a gate
region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters..
Length = 180
Score = 26.9 bits (60), Expect = 4.8
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 2 NSGLFISFEGIEGAGKTTHISLLKRFLQRKNYDVHVTREP-GGTPAAEAARHV 53
+G + G GAGK+T + L L+ + ++ + + E AR +
Sbjct: 23 EAGEIVGILGPNGAGKSTLLKTLAGLLKPSSGEILLDGKDLASLSPKELARKI 75
>gnl|CDD|48380 cd03116, MobB, Molybdenum is an essential trace element in the
form of molybdenum cofactor (Moco) which is associated
with the metabolism of nitrogen, carbon and sulfur by
redox active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe
and mog. The mob locus contains mobA and mobB genes.
MobB catalyzes the attachment of the guanine
dinucleotide to molybdopterin..
Length = 159
Score = 26.7 bits (59), Expect = 4.9
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 7 ISFEGIEGAGKTTHISLLKRFLQRKNYDVHV 37
I F G G+GKTT + L L + V V
Sbjct: 4 IGFVGYSGSGKTTLLEKLIPALSARGLRVAV 34
>gnl|CDD|133067 cd03855, M14_ASTE, Peptidase M14 Succinylglutamate desuccinylase
(ASTE, also known as N-succinyl-L-glutamate
amidohydrolase, N2-succinylglutamate desuccinylase, and
SGDS; EC 3.5.1.96) belongs to the Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily of
the M14 family of metallocarboxypeptidases. This group
includes succinylglutamate desuccinylase that catalyzes
the fifth and last step in arginine catabolism by the
arginine succinyltransferase pathway. It hydrolyzes
N-succinyl-L-glutamate to succinate and L-glutamate.
Length = 322
Score = 26.7 bits (60), Expect = 5.0
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 44 TPAAEAARHVLLSCGV 59
TPAA A + +++S GV
Sbjct: 36 TPAAPATKAIVISAGV 51
>gnl|CDD|73010 cd03251, ABCC_MsbA, MsbA is an essential ABC transporter, closely
related to eukaryotic MDR proteins. ABC transporters
are a large family of proteins involved in the
transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins..
Length = 234
Score = 26.7 bits (59), Expect = 5.2
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 5/35 (14%)
Query: 1 MNSGLFISFEGIEGAGKTTHISLLKRFLQRKNYDV 35
+ +G ++ G G+GK+T ++L+ RF YDV
Sbjct: 25 IPAGETVALVGPSGSGKSTLVNLIPRF-----YDV 54
>gnl|CDD|39436 KOG4235, KOG4235, KOG4235, Mitochondrial thymidine kinase
2/deoxyguanosine kinase [Nucleotide transport and
metabolism].
Length = 244
Score = 26.6 bits (58), Expect = 6.0
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 10 EGIEGAGKTTHISLLKRFLQRKNYDVHVTREP 41
EG GK+T L FL + + V EP
Sbjct: 28 EGNIAVGKST---FLNFFLNKTYEEWEVLTEP 56
>gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
related GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 26.4 bits (58), Expect = 6.3
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 7 ISFEGIEGAGKTTHISLLKRFLQRKNYDVHV 37
I G+ GAGK+T I L R L+ + + V V
Sbjct: 54 IGITGVPGAGKSTLIEALGRELRERGHRVAV 84
>gnl|CDD|38125 KOG2914, KOG2914, KOG2914, Predicted haloacid-halidohydrolase and
related hydrolases [General function prediction only].
Length = 222
Score = 26.4 bits (58), Expect = 6.5
Identities = 17/61 (27%), Positives = 22/61 (36%), Gaps = 6/61 (9%)
Query: 13 EGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPAAEAARHVL----LSCGVDEFGAEAEA 68
E LL R+ K Y V + G +EAAR + +EF E E
Sbjct: 25 EDLYTEAWQELLDRY--GKPYPWDVKVKSMGKRTSEAARLFVKKLPDPVSREEFNKEEEE 82
Query: 69 I 69
I
Sbjct: 83 I 83
>gnl|CDD|48378 cd03114, ArgK-like, The function of this protein family is
unkown. The protein sequences are similar to the ArgK
protein in E. coli. ArgK protein is a membrane ATPase
which is required for transporting arginine, ornithine
and lysine into the cells by the arginine and ornithine
(AO system) and lysine, arginine and ornithine (LAO)
transport systems..
Length = 148
Score = 26.3 bits (58), Expect = 6.8
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 7 ISFEGIEGAGKTTHISLLKRFLQRKNYDVHV 37
I G+ GAGK+T I L L+ + V V
Sbjct: 2 IGITGVPGAGKSTLIDALITALRARGKRVAV 32
>gnl|CDD|110005 pfam00972, Flavi_NS5, Flavivirus RNA-directed RNA polymerase.
Flaviviruses produce a polyprotein from the ssRNA
genome. This protein is also known as NS5. This
RNA-directed RNA polymerase possesses a number of short
regions and motifs homologous to other RNA-directed RNA
polymerases.
Length = 649
Score = 26.3 bits (58), Expect = 7.4
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 12/37 (32%)
Query: 142 IGLKRVQ--NRYSLRESACLD----------YFERKD 166
IG R+ +S+RE+ACL YF R+D
Sbjct: 488 IGRARISPGAGWSIRETACLSKAYAQMWSLMYFHRRD 524
>gnl|CDD|33436 COG3638, COG3638, ABC-type phosphate/phosphonate transport system,
ATPase component [Inorganic ion transport and
metabolism].
Length = 258
Score = 26.3 bits (58), Expect = 7.7
Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 6/87 (6%)
Query: 1 MNSGLFISFEGIEGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPAAEAARHVLLSCGVD 60
+N G ++ G GAGK+T + L + + ++ + R + G
Sbjct: 27 INQGEMVAIIGPSGAGKSTLLRSLNGLVDPTSGEILFNGVQITKLKGKELRKLRRDIG-- 84
Query: 61 EFGAEAEAIVFAAARLDHVENVIRPAL 87
+ +V RL +ENV+ L
Sbjct: 85 -MIFQQFNLV---PRLSVLENVLLGRL 107
>gnl|CDD|143502 cd06829, PLPDE_III_CANSDC, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Carboxynorspermidine
Decarboxylase. Carboxynorspermidine decarboxylase
(CANSDC) catalyzes the decarboxylation of
carboxynorspermidine, the last step in the biosynthesis
of norspermidine. It is homologous to eukaryotic
ornithine decarboxylase (ODC) and diaminopimelate
decarboxylase (DapDC), which are fold type III
PLP-dependent enzymes that contain an N-terminal
PLP-binding TIM-barrel domain and a C-terminal
beta-sandwich domain, similar to bacterial alanine
racemases. Based on this similarity, CANSDC may require
homodimer formation and the presence of the PLP cofactor
for its catalytic activity.
Length = 346
Score = 26.0 bits (58), Expect = 7.8
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 21 ISLLKRFLQRKNYDVHVTREPG 42
I+L+KRF ++ Y V V EPG
Sbjct: 211 IALIKRFKEK--YGVEVYLEPG 230
>gnl|CDD|176119 cd08428, PBP2_IciA_ArgP, The C-terminal substrate binding domain of
LysR-type transcriptional regulator, ArgP (IciA), for
arginine exporter (ArgO); contains the type 2
periplasmic binding fold. The inhibitor of chromosomal
replication (iciA) protein encoded by Mycobacterium
tuberculosis, which is implicated in chromosome
replication initiation in vitro, has been identified as
arginine permease (ArgP), a LysR-type transcriptional
regulator for arginine outward transport, based on the
same amino sequence and similar DNA binding targets. Arp
has been shown to regulate various targets including
DnaA (replication), ArgO (arginine export), dapB (lysine
biosynthesis), and gdhA (glutamate biosynthesis). With
abundant nutrition, ArgP activates the DnaA gene (to
increase replication) and the ArgO (to export redundant
molecules). However, when nutrition supply is limited,
it is suggested that ArgP might function as an inhibitor
of chromosome replication in order to slow replication.
This substrate-binding domain has significant homology
to 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.
Length = 195
Score = 26.1 bits (58), Expect = 7.9
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 162 FERKDVMIHEKRRQIFLDIA-RNQPDRCHIVDSAHSFQSVA 201
F RKD + H+ Q + + P CH V S+ +F +A
Sbjct: 103 FNRKDDL-HQSFLQQHFGLPPGSYP--CHYVPSSEAFVDLA 140
>gnl|CDD|73026 cd03267, ABC_NatA_like, Similar in sequence to NatA, this is the
ATPase component of a bacterial ABC-type Na+ transport
system called NatAB, which catalyzes ATP-dependent
electrogenic Na+ extrusion without mechanically coupled
to proton or K+ uptake. NatB possess six putative
membrane spanning regions at its C-terminus. In B.
subtilis, NatAB is inducible by agents such as ethanol
and protonophores, which lower the protonmotive force
across the membrane. The closest sequence similarity
to NatA is exhibited by DrrA of the two-component
daunomycin- and doxorubicin-efflux system. Hence, the
functional NatAB is presumably assembled with two
copies of the single ATP-binding protein and the single
intergral membrane protein..
Length = 236
Score = 26.0 bits (57), Expect = 7.9
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 3 SGLFISFEGIEGAGKTTHISLLKRFLQRKNYDVHV 37
G + F G GAGKTT + +L LQ + +V V
Sbjct: 46 KGEIVGFIGPNGAGKTTTLKILSGLLQPTSGEVRV 80
>gnl|CDD|72987 cd03228, ABCC_MRP_Like, The MRP (Mutidrug Resistance
Protein)-like transporters are involved in drug,
peptide, and lipid export. They belong to the
subfamily C of the ATP-binding cassette (ABC)
superfamily of transport proteins. The ABCC subfamily
contains transporters with a diverse functional
spectrum that includes ion transport, cell surface
receptor, and toxin secretion activities. The MRP-like
family, simlar to all ABC proteins, have a common
four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins..
Length = 171
Score = 26.1 bits (58), Expect = 8.2
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 2 NSGLFISFEGIEGAGKTTHISLLKRFLQ 29
G ++ G G+GK+T + LL R
Sbjct: 26 KPGEKVAIVGPSGSGKSTLLKLLLRLYD 53
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an
ATPase enzyme and as a kinase, and phosphorylates
periplasmic binding proteins involved in the LAO
(lysine, arginine, ornithine)/AO transport systems.
Length = 267
Score = 26.2 bits (58), Expect = 8.3
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 7 ISFEGIEGAGKTTHISLLKRFLQRKNYDVHV 37
+ G+ GAGK+T I L L+R+ + V V
Sbjct: 32 VGITGVPGAGKSTLIEALGMELRRRGHRVAV 62
>gnl|CDD|177083 CHL00181, cbbX, CbbX; Provisional.
Length = 287
Score = 26.2 bits (58), Expect = 8.4
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 2 NSGLFISFEGIEGAGKTT 19
N GL +SF G G GKTT
Sbjct: 57 NPGLHMSFTGSPGTGKTT 74
>gnl|CDD|145008 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 26.1 bits (58), Expect = 8.8
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 4/28 (14%)
Query: 11 GIEGAGKTTHISLLKRFLQR-KNYDVHV 37
G GKT +LL+ FL+ + V
Sbjct: 27 GPRRCGKT---ALLREFLEELRELGYRV 51
>gnl|CDD|37264 KOG2053, KOG2053, KOG2053, Mitochondrial inheritance and actin
cytoskeleton organization protein [Cytoskeleton].
Length = 932
Score = 25.7 bits (56), Expect = 9.3
Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 1/60 (1%)
Query: 152 SLRESACLDYFERKDVMIHEKRRQIFLDIARNQPDRCHIVDSAHSFQSVATNILNIVWEL 211
LRE L + V+I I + +Q R + ++ F ++ +W +
Sbjct: 691 VLRELELLL-EQYTSVLIPSASFLIQFPLLESQGVRLGDLLNSLEFLMAVPLLVKDLWSV 749
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.322 0.137 0.397
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,683,254
Number of extensions: 139658
Number of successful extensions: 545
Number of sequences better than 10.0: 1
Number of HSP's gapped: 536
Number of HSP's successfully gapped: 65
Length of query: 225
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 135
Effective length of database: 4,318,927
Effective search space: 583055145
Effective search space used: 583055145
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.4 bits)