RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16874
(227 letters)
>gnl|CDD|178512 PLN02924, PLN02924, thymidylate kinase.
Length = 220
Score = 233 bits (597), Expect = 4e-78
Identities = 95/219 (43%), Positives = 135/219 (61%), Gaps = 18/219 (8%)
Query: 1 MASQIPRGAFIVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLR 60
+S RGA IV EG DRSGK+TQ KLV +L + ++ FPDRT S G +I YL
Sbjct: 9 ESSVESRGALIVLEGLDRSGKSTQCAKLVSFLKGLGVAAELWRFPDRTTSVGQMISAYLS 68
Query: 61 KKIELPDQAAHLLFSANRWEREPTLTKLIEQGITLEIMHSSLENEKNLDQGCTNDRYSFS 120
K +L D+A HLLFSANRWE+ + + ++ G TL + DRYS+S
Sbjct: 69 NKSQLDDRAIHLLFSANRWEKRSLMERKLKSGTTLVV-----------------DRYSYS 111
Query: 121 GVAFSAAKEGMDISWCFQPEKGLPKPDAVLLFKLNEEALQRRKGFGDERYEQTDFQRKVA 180
GVAFSAAK G+D+ WC PE GLP PD VL ++ E R G+G ERYE+ +FQ+KVA
Sbjct: 112 GVAFSAAK-GLDLEWCKAPEVGLPAPDLVLYLDISPEEAAERGGYGGERYEKLEFQKKVA 170
Query: 181 ENYEKLKDNIWIDIDADKDIDTLGLIVKDIVIDTIKKSQ 219
+ ++ L+D+ W IDA + I+ + ++++V+DT+++
Sbjct: 171 KRFQTLRDSSWKIIDASQSIEEVEKKIREVVLDTVQRCL 209
>gnl|CDD|223203 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 123 bits (311), Expect = 4e-35
Identities = 67/225 (29%), Positives = 101/225 (44%), Gaps = 37/225 (16%)
Query: 7 RGAFIVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLRKKIE-L 65
+G FIV EG D +GKTTQA+ L + L + I P T G I E L E L
Sbjct: 2 KGMFIVIEGIDGAGKTTQAELLKERLEERGIKVVLTREPGGT-PIGEKIRELLLNGEEKL 60
Query: 66 PDQAAHLLFSANRWEREPTLTKLIEQGITLEIMHSSLENEKNLDQGCT--NDRYSFSGVA 123
+A LLF+A+R + +E+ I + L +G DRY S +A
Sbjct: 61 SPKAEALLFAADRAQ-------HLEEVI-----------KPALKEGKVVICDRYVDSSLA 102
Query: 124 FSAAKEGMDISWCFQPEK---GLPKPDAVLLFKLN-EEALQRRKGFGD--ERYEQTD--F 175
+ G+D+ W + G KPD L + E AL+R + G+ +R+E+ D F
Sbjct: 103 YQGGGRGLDLDWVLALNEFAPGGLKPDLTLYLDVPPEVALERIRKRGELRDRFEKEDDEF 162
Query: 176 QRKVAENYEKLKDNI---WIDIDADKDIDTLGLIVKDIVIDTIKK 217
KV E Y +L I IDA + ++ V + ++ +K+
Sbjct: 163 LEKVREGYLELAAKFPERIIVIDASRPLEE----VHEEILKILKE 203
>gnl|CDD|216936 pfam02223, Thymidylate_kin, Thymidylate kinase.
Length = 186
Score = 115 bits (291), Expect = 2e-32
Identities = 63/208 (30%), Positives = 87/208 (41%), Gaps = 32/208 (15%)
Query: 13 FEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLRKKIELPDQAAHL 72
EG D +GKTTQA+ L + L + I G I E L + EL L
Sbjct: 1 IEGLDGAGKTTQAELLKERLKEQGIKVVL-TREPGGTPIGEKIRELLLRNEELSPLTEAL 59
Query: 73 LFSANRWEREPTLTKLIEQGITLEIMHSSLENEKNLDQGCT--NDRYSFSGVAFSAAKEG 130
LF+A+R E +E+ I + L QG T DRY FS +A+ A G
Sbjct: 60 LFAADRIE-------HLEEKI-----------KPALKQGKTVICDRYLFSSIAYQGAAGG 101
Query: 131 MDIS--WCFQPEKGLPKPDAVLLFKLNEEALQRRKGFGDERY----EQTDFQRKVAENYE 184
+ + P+ PKPD L ++ E +R E EQ DF RKV E Y
Sbjct: 102 LGLDLVLSLNPDVPGPKPDLTFLLDVDPEVALKRLRRRGELDEFEFEQLDFLRKVRERYL 161
Query: 185 KL--KDNIWIDIDADKDIDTLGLIVKDI 210
+L D + IDA I+ + ++I
Sbjct: 162 ELAKDDERILIIDASNSIE---EVHEEI 186
>gnl|CDD|161676 TIGR00041, DTMP_kinase, thymidylate kinase. Function:
phosphorylation of DTMP to form DTDP in both de novo and
salvage pathways of DTTP synthesis. Catalytic activity:
ATP + thymidine 5'-phosphate = ADP + thymidine
5'-diphosphate [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 195
Score = 98.6 bits (246), Expect = 1e-25
Identities = 63/213 (29%), Positives = 91/213 (42%), Gaps = 39/213 (18%)
Query: 7 RGAFIVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLRK----- 61
RG FIV EG D +GKTTQA L L +N F P G I E +R+
Sbjct: 2 RGMFIVIEGIDGAGKTTQANLLKKLLQENGYDVLFTREP-----GGTPIGEKIRELLLNE 56
Query: 62 -KIELPDQAAHLLFSANRWEREPTLTKLIEQGITLEIMHSSLENEKNLDQGC--TNDRYS 118
L D+A LLF+A+R E +E I + L +G +DRY
Sbjct: 57 NDEPLTDKAEALLFAADRHE-------HLEDKI-----------KPALAEGKLVISDRYV 98
Query: 119 FSGVAFSAAKEGMDIS--WCFQPEKGLPKPDAVLLFKLN-EEALQRRKGFGD---ERYEQ 172
FS +A+ G+D + PD + ++ E AL+R + G+ E +E+
Sbjct: 99 FSSIAYQGGARGIDEDLVLELNEDALGDMPDLTIYLDIDPEVALERLRKRGELDREEFEK 158
Query: 173 TDFQRKVAENYEKLKDNI--WIDIDADKDIDTL 203
DF KV + Y +L D IDA ++ +
Sbjct: 159 LDFFEKVRQRYLELADKEKSIHVIDATNSVEEV 191
>gnl|CDD|238835 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 = 85.4 bits (212), Expect = 1e-20
Identities = 56/228 (24%), Positives = 88/228 (38%), Gaps = 49/228 (21%)
Query: 10 FIVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLRKKIELPDQA 69
FIVFEG D +GKTT + L + L P G I E +R+ + P+
Sbjct: 2 FIVFEGIDGAGKTTLIELLAERLEARGYEVVLTREP-----GGTPIGEAIRELLLDPEDE 56
Query: 70 AH------LLFSANRWEREPTLTKLIEQGITLEIMHSSLENEKNLDQG----CTNDRYSF 119
LLF+A+R + +E+ I + L +G DR+
Sbjct: 57 KMDPRAELLLFAADR-------AQHVEEVI-----------KPALARGKIVLS--DRFVD 96
Query: 120 SGVAFSAAKEGMD---ISWCFQPEKGLPKPDAVLLFKLN-EEALQR---RKGFGDERYEQ 172
S +A+ A G+ I G KPD +L ++ E L R R + E
Sbjct: 97 SSLAYQGAGRGLGEALIEALNDLATGGLKPDLTILLDIDPEVGLARIEARGRDDRDEQEG 156
Query: 173 TDFQRKVAENYEKL---KDNIWIDIDADKDIDTLGLIVKDIVIDTIKK 217
+F +V E Y +L + I IDA + ++ V ++ I +
Sbjct: 157 LEFHERVREGYLELAAQEPERIIVIDASQPLE----EVLAEILKAILE 200
>gnl|CDD|234814 PRK00698, tmk, thymidylate kinase; Validated.
Length = 205
Score = 84.1 bits (209), Expect = 4e-20
Identities = 60/223 (26%), Positives = 94/223 (42%), Gaps = 43/223 (19%)
Query: 6 PRGAFIVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLRKKIEL 65
RG FI EG D +GK+TQ + L + L + F P G + E LR+ +
Sbjct: 1 MRGMFITIEGIDGAGKSTQIELLKELLEQQGRDVVFTREP-----GGTPLGEKLRELLLD 55
Query: 66 PDQAAH-----LLFSANRWEREPTLTKLIEQGITLEIMHSSLENEKNLDQGCT--NDRYS 118
P++ LLF A R + +E+ I + L +G +DR+
Sbjct: 56 PNEEMDDKTELLLFYAARAQ-------HLEEVI-----------KPALARGKWVISDRFI 97
Query: 119 FSGVAFSAAKEGMDISWCFQPEK---GLPKPDAVLLFKLN-EEALQRRKGFGD-ERYEQ- 172
S +A+ G+DI G +PD L + E L R + G+ +R EQ
Sbjct: 98 DSSLAYQGGGRGLDIDLLLALNDFALGGFRPDLTLYLDVPPEVGLARIRARGELDRIEQE 157
Query: 173 -TDFQRKVAENYEKL--KDNIWID-IDADKDIDTLGLIVKDIV 211
DF +V E Y +L K+ I IDA + ++ + +DI+
Sbjct: 158 GLDFFERVREGYLELAEKEPERIVVIDASQSLEE---VHEDIL 197
>gnl|CDD|184430 PRK13975, PRK13975, thymidylate kinase; Provisional.
Length = 196
Score = 79.8 bits (197), Expect = 2e-18
Identities = 70/210 (33%), Positives = 98/210 (46%), Gaps = 38/210 (18%)
Query: 10 FIVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLRKKIELPDQA 69
FIVFEG D SGKTTQAK L + LN F G +I E L + +
Sbjct: 4 FIVFEGIDGSGKTTQAKLLAEKLNA------FWTCEPTDGKIGKLIREILSGS-KCDKET 56
Query: 70 AHLLFSANRWEREPTLTKLIEQGITLEIMHSSLENEKNLDQGCTNDRYSFSGVAFSAAKE 129
LLF+A+R E K IE E+ K D C DRY +S +A+ + +
Sbjct: 57 LALLFAADRVEH----VKEIE------------EDLKKRDVVC--DRYVYSSIAYQSV-Q 97
Query: 130 GMDISWCFQPEKGLPKPDAVLLFKLN-EEALQRRKGFGDERYEQTDFQRKVAENYEKLKD 188
G+D + + + KPD V L ++ EEAL+R + E +E+ +F +KV E Y +L
Sbjct: 98 GIDEDFIYSINRYAKKPDLVFLLDVDIEEALKRMETRDKEIFEKKEFLKKVQEKYLEL-- 155
Query: 189 NIWIDIDADKDIDTLGLIVKDIVIDTIKKS 218
+ +K + G IVIDT KS
Sbjct: 156 -----ANNEKFMPKYGF----IVIDTTNKS 176
>gnl|CDD|172477 PRK13974, PRK13974, thymidylate kinase; Provisional.
Length = 212
Score = 58.9 bits (143), Expect = 1e-10
Identities = 60/235 (25%), Positives = 107/235 (45%), Gaps = 46/235 (19%)
Query: 7 RGAFIVFEGCDRSGKTTQAKKLVDYLNKNN-IPSQFVNFPDRTIST----GHIIDEYLRK 61
+G FIV EG D GKTTQ L +L + +P + I T G ++ + LR+
Sbjct: 2 KGKFIVLEGIDGCGKTTQIDHLSKWLPSSGLMPKG-----AKLIITREPGGTLLGKSLRE 56
Query: 62 KI------ELPDQAAHL-LFSANRWEREPTLTKLIEQGITLEIMHSSLENEKNLDQG--C 112
+ P A L L++A+R + ++K+I L+ G
Sbjct: 57 LLLDTSKDNSPSPLAELLLYAADRAQH---VSKIIRPA---------------LENGDWV 98
Query: 113 TNDRYSFSGVAFSAAKEGMDISWCFQPE----KGLPKPDAVLLFKLN-EEALQRRKGFGD 167
+DR+S S +A+ G+D+ E +GL PD +++ EE+++RRK
Sbjct: 99 ISDRFSGSTLAYQGYGRGLDLELIKNLESIATQGL-SPDLTFFLEISVEESIRRRKNRKP 157
Query: 168 ERYEQ--TDFQRKVAENYEKL-KDNIWIDIDADKDIDTLGLIVKDIVIDTIKKSQ 219
+R E +F +VAE + + ++ W I AD+ I+T+ +K+ +++ +
Sbjct: 158 DRIEAEGIEFLERVAEGFALIAEERNWKVISADQSIETISNEIKETLLNNFSNKK 212
>gnl|CDD|236133 PRK07933, PRK07933, thymidylate kinase; Validated.
Length = 213
Score = 43.8 bits (104), Expect = 2e-05
Identities = 53/219 (24%), Positives = 82/219 (37%), Gaps = 44/219 (20%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFP--DRTISTGHIIDEYLRKKI-ELPD 67
I EG D +GK T + L L + FP R++ + E L + +L D
Sbjct: 3 IAIEGVDGAGKRTLTEALRAALEARGRSVATLAFPRYGRSV-HADLAAEALHGRHGDLAD 61
Query: 68 Q--AAHLLFSANRWEREPTLTKLIEQGITLEIMHSSLENEKNLDQGCTNDRYSFSGVAFS 125
A LF+ +R L L+ + + DRY S A+S
Sbjct: 62 SVYAMATLFALDRAGARDELAGLLAAHDVVIL-----------------DRYVASNAAYS 104
Query: 126 AAKEGMD-----ISWCFQPEK---GLPKPDAVLLFKLNEE-ALQRRKGFGDE-------R 169
AA+ D ++W + E GLP PD +L + E A +R + +
Sbjct: 105 AARLHQDADGEAVAWVAELEFGRLGLPVPDLQVLLDVPVELAAERARRRAAQDADRARDA 164
Query: 170 YEQTD-FQRKVAENYEKL-KDNI---WIDIDADKDIDTL 203
YE+ D Q++ Y +L W+ +D D D L
Sbjct: 165 YERDDGLQQRTGAVYAELAAQGWGGPWLVVDPDVDPAAL 203
>gnl|CDD|184429 PRK13973, PRK13973, thymidylate kinase; Provisional.
Length = 213
Score = 39.5 bits (93), Expect = 5e-04
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 7 RGAFIVFEGCDRSGKTTQAKKLVDYLNK 34
RG FI FEG + +GK+TQ + L + L
Sbjct: 2 RGRFITFEGGEGAGKSTQIRLLAERLRA 29
Score = 28.0 bits (63), Expect = 3.8
Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 16/80 (20%)
Query: 145 KPDAVLLFKLNEE-----ALQRRKGFGDERYE--QTDFQRKVAENYEKLKDNIWID---- 193
PD L+ + E A +RR +R+E F K E + ++ +
Sbjct: 128 MPDLTLILDIPAEVGLERAAKRRGSDTPDRFEKEDLAFHEKRREAFLQIAAQ---EPERC 184
Query: 194 --IDADKDIDTLGLIVKDIV 211
IDA + + + V
Sbjct: 185 VVIDATASPEAVAAEIWAAV 204
>gnl|CDD|237574 PRK13976, PRK13976, thymidylate kinase; Provisional.
Length = 209
Score = 38.2 bits (89), Expect = 0.001
Identities = 15/25 (60%), Positives = 19/25 (76%)
Query: 10 FIVFEGCDRSGKTTQAKKLVDYLNK 34
FI FEG D SGKTTQ++ L +YL+
Sbjct: 2 FITFEGIDGSGKTTQSRLLAEYLSD 26
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield
adenosine diphosphates (ADP). This enzyme is required
for the biosynthesis of ADP and is essential for
homeostasis of adenosine phosphates.
Length = 194
Score = 36.4 bits (85), Expect = 0.004
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 12/60 (20%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLRKKIELPDQAA 70
I+ G SGK TQA++L K +P ISTG ++ E + EL +A
Sbjct: 2 ILLLGPPGSGKGTQAERLAK---KYGLPH---------ISTGDLLREEIASGTELGKKAK 49
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 34.1 bits (79), Expect = 0.042
Identities = 13/34 (38%), Positives = 16/34 (47%)
Query: 10 FIVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVN 43
+ F G SGKTT K L D+L + VN
Sbjct: 4 IVFFLGTAGSGKTTLTKALSDWLEEQGYDVAIVN 37
>gnl|CDD|233369 TIGR01351, adk, adenylate kinase. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family are
known or believed to be adenylate kinase. However, some
members accept other nucleotide triphosphates as donors,
may be unable to use ATP, and may fail to complement
adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 210
Score = 33.7 bits (78), Expect = 0.049
Identities = 32/160 (20%), Positives = 55/160 (34%), Gaps = 49/160 (30%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLRKKIELPDQAA 70
+V G SGK TQAK++ K +P ISTG ++ ++ L +A
Sbjct: 2 LVLLGPPGSGKGTQAKRIA---EKYGLPH---------ISTGDLLRAEIKAGTPLGKKAK 49
Query: 71 HLLFSANRWEREPTLTKLIEQG------ITLEIMHSSLENEKNLDQGCTNDRY--SFSGV 122
+ +E+G I +++ L ++ + G D + + S
Sbjct: 50 ----------------EYMEKGELVPDEIVNQLVKERLTQNQDNENGFILDGFPRTLSQA 93
Query: 123 AFSAAKEGMDISWCFQPEKGLPKPDAVLLFKLNEEALQRR 162
A K DAV+ + +E L R
Sbjct: 94 EALDALLKE-------------KIDAVIELDVPDEELVER 120
>gnl|CDD|180682 PRK06761, PRK06761, hypothetical protein; Provisional.
Length = 282
Score = 33.2 bits (76), Expect = 0.074
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFV 42
I+ EG GK+T AK L D L++N I +
Sbjct: 6 IIIEGLPGFGKSTTAKMLNDILSQNGIEVELY 37
>gnl|CDD|219839 pfam08433, KTI12, Chromatin associated protein KTI12. This is a
family of chromatin associated proteins which interact
with the Elongator complex, a component of the
elongating form of RNA polymerase II. The Elongator
complex has histone acetyltransferase activity.
Length = 266
Score = 32.3 bits (74), Expect = 0.14
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVN 43
I+ G SGK+T+AK+L YL + ++
Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEKGYDVIVIS 34
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 29.6 bits (67), Expect = 0.22
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNI 37
I G SGK+T AKKL + L ++
Sbjct: 2 IAITGGSGSGKSTVAKKLAEQLGGRSV 28
>gnl|CDD|234711 PRK00279, adk, adenylate kinase; Reviewed.
Length = 215
Score = 30.9 bits (71), Expect = 0.33
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 12/34 (35%)
Query: 19 SGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTG 52
+GK TQAK + + K IP ISTG
Sbjct: 11 AGKGTQAKFIAE---KYGIP---------HISTG 32
>gnl|CDD|165262 PHA02953, PHA02953, IEV and EEV membrane glycoprotein; Provisional.
Length = 170
Score = 30.5 bits (69), Expect = 0.41
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 185 KLKDNIWIDIDADKDIDTLGLIVKDIVIDTIKKSQ 219
K K+N W+DI+ +K +D + K+ + IK
Sbjct: 106 KKKNNRWLDINTNKTVD----MNKNTELKKIKSKT 136
>gnl|CDD|180871 PRK07191, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 456
Score = 30.2 bits (68), Expect = 0.88
Identities = 13/31 (41%), Positives = 15/31 (48%)
Query: 92 GITLEIMHSSLENEKNLDQGCTNDRYSFSGV 122
IT HS LEN +N+ SFSGV
Sbjct: 389 AITSNQNHSELENAENVRNQAERYWESFSGV 419
>gnl|CDD|227341 COG5008, PilU, Tfp pilus assembly protein, ATPase PilU [Cell
motility and secretion / Intracellular trafficking and
secretion].
Length = 375
Score = 29.7 bits (67), Expect = 1.2
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 15/50 (30%)
Query: 6 PRGAFIVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHII 55
RG ++ G SGK+T ++ Y NKN STGHII
Sbjct: 126 KRG-LVIIVGATGSGKSTTMAAMIGYRNKN--------------STGHII 160
>gnl|CDD|233406 TIGR01420, pilT_fam, pilus retraction protein PilT. This model
represents the PilT subfamily of proteins related to
GspE, a protein involved in type II secretion (also
called the General Secretion Pathway). PilT is an
apparent cytosolic ATPase associated with type IV pilus
systems. It is not required for pilin biogenesis, but is
required for twitching motility and social gliding
behaviors, shown in some species, powered by pilus
retraction. Members of this family may be found in some
species that type IV pili but have related structures
for DNA uptake and natural transformation [Cell
envelope, Surface structures, Cellular processes,
Chemotaxis and motility].
Length = 343
Score = 29.2 bits (66), Expect = 1.6
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 6 PRGAFIVFEGCDRSGKTTQAKKLVDYLNKN 35
PRG I+ G SGK+T ++DY+NKN
Sbjct: 121 PRG-LILVTGPTGSGKSTTLASMIDYINKN 149
>gnl|CDD|179433 PRK02496, adk, adenylate kinase; Provisional.
Length = 184
Score = 28.9 bits (65), Expect = 1.8
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 12/59 (20%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLRKKIELPDQA 69
++F G +GK TQA L ++L +IP ISTG I+ + ++++ L +A
Sbjct: 4 LIFLGPPGAGKGTQAVVLAEHL---HIPH---------ISTGDILRQAIKEQTPLGIKA 50
>gnl|CDD|224742 COG1829, COG1829, Predicted archaeal kinase (sugar kinase
superfamily) [General function prediction only].
Length = 283
Score = 28.9 bits (65), Expect = 2.0
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 49 ISTGHIIDEYLRKKIELPDQAAHLLFSANRWEREPTLTKLIEQ 91
+ST +I + + +KI + L + PTL +E+
Sbjct: 172 LSTKSVITDEVVRKIN--EAGKRAL---AELLKNPTLENFMEE 209
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 27.9 bits (63), Expect = 2.3
Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNF---PDRTISTGHIIDEYLRKKIE 64
IV G + GKTT + + L NI ++N ++ +++E+L+ +
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENIL--YINLDDPRFLRLALLDLLEEFLKLLLP 59
>gnl|CDD|239389 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 = 28.3 bits (64), Expect = 2.7
Identities = 12/26 (46%), Positives = 13/26 (50%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNN 36
I+ G GKTT A KL YL K
Sbjct: 3 ILLVGLQGVGKTTTAAKLALYLKKKG 28
>gnl|CDD|215243 PLN02444, PLN02444, HMP-P synthase.
Length = 642
Score = 28.7 bits (64), Expect = 2.8
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 8/40 (20%)
Query: 139 PEKGLPKPDAVLLFKLNEEALQRRKGFGDERYEQTDFQRK 178
P GLPK L +E + RR+ G RY Q + ++
Sbjct: 138 PRIGLPK--------LRKEWIDRREKLGTPRYTQMYYAKQ 169
>gnl|CDD|213237 cd03270, ABC_UvrA_I, ATP-binding cassette domain I of the
excision repair protein UvrA. Nucleotide excision
repair in eubacteria is a process that repairs DNA
damage by the removal of a 12-13-mer oligonucleotide
containing the lesion. Recognition and cleavage of the
damaged DNA is a multistep ATP-dependent reaction that
requires the UvrA, UvrB, and UvrC proteins. Both UvrA
and UvrB are ATPases, with UvrA having two ATP binding
sites, which have the characteristic signature of the
family of ABC proteins, and UvrB having one ATP binding
site that is structurally related to that of helicases.
Length = 226
Score = 28.0 bits (63), Expect = 3.1
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 5 IPRGAFIVFEGCDRSGKTTQA 25
IPR +V G SGK++ A
Sbjct: 18 IPRNKLVVITGVSGSGKSSLA 38
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 27.6 bits (62), Expect = 4.0
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 12/44 (27%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHI 54
I+ G +GK+T AKKL K +P + TG I
Sbjct: 3 ILILGPPGAGKSTLAKKLA---KKLGLPH---------LDTGDI 34
>gnl|CDD|233062 TIGR00630, uvra, excinuclease ABC, A subunit. This family is a
member of the ABC transporter superfamily of proteins
of which all members for which functions are known
except the UvrA proteins are involved in the transport
of material through membranes. UvrA orthologs are
involved in the recognition of DNA damage as a step in
nucleotide excision repair. 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 = 925
Score = 28.1 bits (63), Expect = 4.3
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 5 IPRGAFIVFEGCDRSGKTTQA 25
IPR +V G SGK++ A
Sbjct: 19 IPRDKLVVITGLSGSGKSSLA 39
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and
metabolism].
Length = 218
Score = 27.6 bits (62), Expect = 4.5
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 1 MASQIPRGAFIVFEGCDRSGKTTQAKKLVDYLNKNNI 37
M + + I G SGKTT AK+L + L +
Sbjct: 1 MMKKPEKVIIIGIAGGSGSGKTTVAKELSEQLGVEKV 37
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 27.8 bits (62), Expect = 4.7
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 1 MASQIPRGAFIVFEGCDRSGKTT--QAKKLVDYLNKNNIP 38
+ +IP G IV GKT KK +D L K IP
Sbjct: 185 VLQRIPDGVVIV----TTPGKTALEDVKKAIDMLEKAGIP 220
>gnl|CDD|238988 cd02030, NDUO42, NADH:Ubiquinone oxioreductase, 42 kDa (NDUO42)
is a family of proteins that are highly similar to
deoxyribonucleoside kinases (dNK). Members of this
family have been identified as one of the subunits of
NADH:Ubiquinone oxioreductase (complex I), a
multi-protein complex located in the inner
mitochondrial membrane. The main function of the
complex is to transport electrons from NADH to
ubiquinone, which is accompanied by the translocation
of protons from the mitochondrial matrix to the inter
membrane space.
Length = 219
Score = 27.7 bits (62), Expect = 4.8
Identities = 14/47 (29%), Positives = 21/47 (44%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDE 57
I +G SGK AK+L + L P +++ D T G +D
Sbjct: 2 ITVDGNIASGKGKLAKELAEKLGMKYFPEAGIHYLDSTTGDGKPLDP 48
>gnl|CDD|238982 cd02024, NRK1, Nicotinamide riboside kinase (NRK) is an enzyme
involved in the metabolism of nicotinamide adenine
dinucleotide (NAD+). This enzyme catalyzes the
phosphorylation of nicotinamide riboside (NR) to form
nicotinamide mononucleotide (NMN). It defines the NR
salvage pathway of NAD+ biosynthesis in addition to the
pathways through nicotinic acid mononucleotide (NaMN).
This enzyme can also phosphorylate the anticancer drug
tiazofurin, which is an analog of nicotinamide
riboside.
Length = 187
Score = 27.3 bits (61), Expect = 4.9
Identities = 10/18 (55%), Positives = 10/18 (55%)
Query: 15 GCDRSGKTTQAKKLVDYL 32
G SGKTT AK L L
Sbjct: 6 GVTNSGKTTLAKLLQRIL 23
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 27.1 bits (61), Expect = 5.5
Identities = 12/26 (46%), Positives = 13/26 (50%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNN 36
I+ G SGKTT KL YL K
Sbjct: 4 ILLVGLQGSGKTTTIAKLAAYLKKQG 29
>gnl|CDD|183784 PRK12838, PRK12838, carbamoyl phosphate synthase small subunit;
Reviewed.
Length = 354
Score = 27.5 bits (62), Expect = 5.7
Identities = 9/30 (30%), Positives = 13/30 (43%)
Query: 9 AFIVFEGCDRSGKTTQAKKLVDYLNKNNIP 38
IV+E + L D+L + NIP
Sbjct: 77 GVIVYELSREGSHYRAKQSLDDFLKEWNIP 106
>gnl|CDD|180442 PRK06175, PRK06175, L-aspartate oxidase; Provisional.
Length = 433
Score = 27.7 bits (62), Expect = 6.1
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 175 FQRKVAENYEKLKDNIWIDI----DADKDIDTLGLIVKDIVIDTIKK 217
F ++ AE DNI ++I D++ L+ K I+I I+K
Sbjct: 375 FSKRGAEKINSEIDNIKLNITKVYTLKHDVEYYSLLNKKIIIKEIEK 421
>gnl|CDD|185672 cd00418, GlxRS_core, catalytic core domain of glutamyl-tRNA and
glutaminyl-tRNA synthetase. Glutamyl-tRNA
synthetase(GluRS)/Glutaminyl-tRNA synthetase (GlnRS)
cataytic core domain. These enzymes attach Glu or Gln,
respectively, to the appropriate tRNA. Like other class
I tRNA synthetases, they aminoacylate the 2'-OH of the
nucleotide at the 3' end of the tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. These enzymes function as monomers. Archaea,
cellular organelles, and some bacteria lack GlnRS. In
these cases, the "non-discriminating" form of GluRS
aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu,
which is converted to Gln when appropriate by a
transamidation enzyme. The discriminating form of GluRS
differs from GlnRS and the non-discriminating form of
GluRS in their C-terminal anti-codon binding domains.
Length = 230
Score = 27.1 bits (60), Expect = 6.5
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 154 LNEEALQRRKGFGDERYEQTDFQRKVAENYEKLKDNI-WIDIDAD 197
N ++ G R E TD +R E E + +++ W+ +D D
Sbjct: 24 FNFAFARKYGGKFILRIEDTDPERSRPEYVESILEDLKWLGLDWD 68
>gnl|CDD|216591 pfam01591, 6PF2K, 6-phosphofructo-2-kinase. This enzyme occurs
as a bifunctional enzyme with
fructose-2,6-bisphosphatase. The bifunctional enzyme
catalyzes both the synthesis and degradation of
fructose-2,6-bisphosphate, a potent regulator of
glycolysis. This enzyme contains a P-loop motif.
Length = 219
Score = 27.3 bits (61), Expect = 6.6
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNF 44
IV G GKT +KKL YLN +P++ N
Sbjct: 13 IVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNV 46
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 27.1 bits (61), Expect = 7.0
Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 18/80 (22%)
Query: 27 KLVDYLNKNNIPSQFVNF-----PDRTISTGHI--IDEYLRKKIELPDQAAHLLFSANRW 79
+L+D L + + V + DR + G I E L+ LP LLFSA
Sbjct: 129 RLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILK---LLPKDRQTLLFSA--- 182
Query: 80 EREPTLTKLIEQGITLEIMH 99
T+ K + + + +
Sbjct: 183 ----TMPKEVRD-LARKFLR 197
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins
in this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 27.0 bits (60), Expect = 7.1
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLRKKIELPD 67
I G SGKTT AK L + L+ I + + F + G + E+L E P+
Sbjct: 3 ITISGPPGSGKTTVAKILAEKLSLKLISAGDI-FRELAAKMGLDLIEFLNYAEENPE 58
>gnl|CDD|163562 TIGR03850, bind_CPR_0540, carbohydrate ABC transporter
substrate-binding protein, CPR_0540 family. Members of
this protein are the substrate-binding protein of a
predicted carbohydrate transporter operon, together with
permease subunits of ABC transporter homology families.
This substrate-binding protein frequently co-occurs in
genomes with a family of disaccharide phosphorylases,
TIGR02336, suggesting that the molecule transported will
include
beta-D-galactopyranosyl-(1->3)-N-acetyl-D-glucosamine
and related carbohydrates. Members of this family are
sporadically strain by strain, often in species with a
human host association, including Propionibacterium
acnes and Clostridium perfringens, and Bacillus cereus
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 437
Score = 27.3 bits (61), Expect = 7.4
Identities = 8/38 (21%), Positives = 21/38 (55%), Gaps = 6/38 (15%)
Query: 164 GFGDERYEQTDFQRKVAENYEKLKDNIWIDIDADKDID 201
G+G + +E+ V E +EK + + +++ K+++
Sbjct: 44 GYGTKMWEE------VVEAFEKSHEGVKVELTVSKNLE 75
>gnl|CDD|237745 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 26.7 bits (59), Expect = 7.8
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 4 QIPRGAFIVFEGCDRSGKTTQAKKLVDYLNKNNIPSQFVNFPDRTISTGHIIDEYLRKKI 63
+ ++F G +GK TQA++L L + +STG I+ +++ +
Sbjct: 2 TQTKNKVVIFLGPPGAGKGTQAERLAQELGL------------KKLSTGDILRDHVARGT 49
Query: 64 ELPDQAAHLL 73
EL +A ++
Sbjct: 50 ELGQRAKPIM 59
>gnl|CDD|115108 pfam06431, Polyoma_lg_T_C, Polyomavirus large T antigen C-terminus.
Length = 417
Score = 27.2 bits (60), Expect = 7.8
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 11/64 (17%)
Query: 1 MASQIPRGAFIVFEGCDRSGKTTQAKKLVDY-----LNKNNIPSQFVNFPDRTISTGHII 55
+ IP+ + +F+G SGKTT A L+D LN N+P + +NF G I
Sbjct: 148 IVYNIPKKRYWLFKGPIDSGKTTLAAALLDLCGGKALNV-NLPLERLNF-----ELGVAI 201
Query: 56 DEYL 59
D+++
Sbjct: 202 DQFM 205
>gnl|CDD|213852 TIGR03707, PPK2_P_aer, polyphosphate kinase 2, PA0141 family.
Members of this protein family are designated
polyphosphate kinase 2 (PPK2) after the characterized
protein in Pseudomonas aeruginosa. This family
comprises one of three well-separated clades in the
larger family described by pfam03976. PA0141 from this
family has been shown capable of operating in reverse,
with GDP preferred (over ADP) as a substrate, producing
GTP (or ATP) by transfer of a phosphate residue from
polyphosphate. Most species with a member of this
family also encode a polyphosphate kinase 1 (PPK1)
[Central intermediary metabolism, Phosphorus
compounds].
Length = 230
Score = 26.8 bits (60), Expect = 8.5
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLN 33
IVFEG D +GK K++ ++LN
Sbjct: 34 IVFEGRDAAGKGGTIKRITEHLN 56
>gnl|CDD|198165 smart01097, CPSase_sm_chain, Carbamoyl-phosphate synthase small
chain, CPSase domain. The carbamoyl-phosphate synthase
domain is in the amino terminus of protein.
Carbamoyl-phosphate synthase catalyses the ATP-dependent
synthesis of carbamyl-phosphate from glutamine or
ammonia and bicarbonate. This important enzyme initiates
both the urea cycle and the biosynthesis of arginine
and/or pyrimidines. The carbamoyl-phosphate synthase
(CPS) enzyme in prokaryotes is a heterodimer of a small
and large chain. The small chain promotes the hydrolysis
of glutamine to ammonia, which is used by the large
chain to synthesise carbamoyl phosphate. The small chain
has a GATase domain in the carboxyl terminus.
Length = 130
Score = 26.2 bits (59), Expect = 9.7
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 9 AFIVFEGCDRSGKTTQAKKLVDYLNKNNIP 38
+V E D + L ++L +N IP
Sbjct: 77 GLVVRELSDEPSNWRSEQSLDEFLKENGIP 106
>gnl|CDD|232857 TIGR00176, mobB, molybdopterin-guanine dinucleotide biosynthesis
protein MobB. This molybdenum cofactor biosynthesis
enzyme is similar to the urease accessory protein UreG
and to the hydrogenase accessory protein HypB, both GTP
hydrolases involved in loading nickel into the
metallocenters of their respective target enzymes
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Molybdopterin].
Length = 155
Score = 26.2 bits (58), Expect = 9.9
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 11 IVFEGCDRSGKTTQAKKLVDYLNKNNIP 38
+ G SGKTT ++LV L
Sbjct: 2 LQIVGPKNSGKTTLIERLVKALKARGYR 29
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
0.317 0.135 0.394
Gapped
Lambda K H
0.267 0.0911 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,822,083
Number of extensions: 1129554
Number of successful extensions: 1401
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1379
Number of HSP's successfully gapped: 98
Length of query: 227
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 134
Effective length of database: 6,812,680
Effective search space: 912899120
Effective search space used: 912899120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.4 bits)