RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780957|ref|YP_003065370.1| dihydrofolate reductase
protein [Candidatus Liberibacter asiaticus str. psy62]
(176 letters)
>gnl|CDD|143949 pfam00186, DHFR_1, Dihydrofolate reductase.
Length = 159
Score = 210 bits (538), Expect = 1e-55
Identities = 74/165 (44%), Positives = 102/165 (61%), Gaps = 6/165 (3%)
Query: 5 EIILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIGRLLPGRTNI 64
I LI A+ +N VIG +PW + DLK FK+LT G P++MG +TF+SIGR LPGRTNI
Sbjct: 1 MISLIVAVDKNGVIGKDNDLPWHLPEDLKHFKALTMGKPIIMGRKTFESIGRPLPGRTNI 60
Query: 65 IITRDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTISLAHTLYITH 124
++TR+ +A + S+ ++L LA+ ++IFIIGG EIY Q + A LY+T
Sbjct: 61 VLTRNPDFKA---EGVEVVHSLEEALALAAGE--EEIFIIGGAEIYKQALPYADRLYLTE 115
Query: 125 IEKEIEGDVFFPSIDSNIWKKQEKEIITSAGEGDDYPTRFVIYDR 169
I+ E EGD FFP ID + W+ +E A E + Y FV Y+R
Sbjct: 116 IDAEFEGDTFFPEIDLSEWELVSRE-EHPADEKNPYDYTFVTYER 159
>gnl|CDD|29264 cd00209, DHFR, Dihydrofolate reductase (DHFR). Reduces
7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH
as a cofactor. This is an essential step in the
biosynthesis of deoxythymidine phosphate since
5,6,7,8-tetrahydrofolate is required to regenerate
5,10-methylenetetrahydrofolate which is then utilized by
thymidylate synthase. Inhibition of DHFR interrupts
thymidilate synthesis and DNA replication, inhibitors of
DHFR (such as Methotrexate) are used in cancer
chemotherapy. 5,6,7,8-tetrahydrofolate also is involved
in glycine, serine, and threonine metabolism and
aminoacyl-tRNA biosynthesis..
Length = 158
Score = 172 bits (437), Expect = 5e-44
Identities = 71/163 (43%), Positives = 94/163 (57%), Gaps = 7/163 (4%)
Query: 6 IILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIGRL-LPGRTNI 64
I LI A+ N VIG +PW + DLK FK TTGNPV+MG +TF+SI R LPGRTNI
Sbjct: 1 ISLIVAVDENGVIGKDNKLPWHLPEDLKHFKKTTTGNPVIMGRKTFESIPRRPLPGRTNI 60
Query: 65 IITRDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTISLAHTLYITH 124
+++R + S+ ++L+LA T ++IF+IGG EIY Q + A LY+T
Sbjct: 61 VLSR--QLDYQDAEGVEVVHSLEEALELAENTV-EEIFVIGGAEIYKQALPYADRLYLTR 117
Query: 125 IEKEIEGDVFFPSIDSNIWKKQEKEIITSAGEGDDYPTRFVIY 167
I E EGD FFP ID + W+ +E + E D Y F Y
Sbjct: 118 IHAEFEGDTFFPEIDESEWELVSEEEVF---EEDGYSYTFETY 157
>gnl|CDD|30611 COG0262, FolA, Dihydrofolate reductase [Coenzyme metabolism].
Length = 167
Score = 137 bits (347), Expect = 1e-33
Identities = 63/170 (37%), Positives = 89/170 (52%), Gaps = 11/170 (6%)
Query: 6 IILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIG---RLLPGRT 62
IILI A++ + VIG +PW + DL FK+ T G PV+MG +T++S+ R LPGR
Sbjct: 2 IILIVAVSLDGVIGRDNSLPWHLPEDLAHFKATTLGKPVIMGRKTYESLPGEWRPLPGRK 61
Query: 63 NIIITRDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTIS--LAHTL 120
NI+++R+ + + SI ++L L K + IFIIGGGE+Y Q + LA L
Sbjct: 62 NIVLSRNPDLKTEGG--VEVVDSIEEALLLLLKEEGEDIFIIGGGELYRQFLPAGLADEL 119
Query: 121 YITHIEKEI-EGDVFFPSIDSNIWKKQEKEIITSAGEGDDYPTRFVIYDR 169
+T I + EGD FP D W+ A E Y F Y+R
Sbjct: 120 ILTIIPVLLGEGDTLFPEGDPADWE---LVSSEDADEKGGYFYTFESYER 166
>gnl|CDD|36538 KOG1324, KOG1324, KOG1324, Dihydrofolate reductase [Coenzyme
transport and metabolism].
Length = 190
Score = 104 bits (260), Expect = 1e-23
Identities = 52/157 (33%), Positives = 90/157 (57%), Gaps = 16/157 (10%)
Query: 8 LIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTG-------NPVVMGYRTFQSI---GRL 57
L+ A++ N IG G +PW + S++K F+ +TT N V+MG +T++SI R
Sbjct: 6 LVVALSPNMGIGKNGDLPWPLPSEMKYFRRVTTSTSDPSKKNAVIMGRKTWESIPEKFRP 65
Query: 58 LPGRTNIIITRDNTRRASVNPEAVLASSILDSLDLASKTGSK----KIFIIGGGEIYAQT 113
LPGR N++++R + L+SS+ +LDL + S +F+IGG E+Y++
Sbjct: 66 LPGRINVVLSRSLKEDFAPTENVFLSSSLESALDLLEEPPSSNSVEMVFVIGGSEVYSEA 125
Query: 114 IS--LAHTLYITHIEKEIEGDVFFPSIDSNIWKKQEK 148
++ ++IT I + E D FFP+ID++ ++K +K
Sbjct: 126 LNSPRCDAIHITEIFQSFECDTFFPAIDTSSYEKWDK 162
>gnl|CDD|30562 COG0213, DeoA, Thymidine phosphorylase [Nucleotide transport and
metabolism].
Length = 435
Score = 30.2 bits (68), Expect = 0.29
Identities = 31/119 (26%), Positives = 48/119 (40%), Gaps = 25/119 (21%)
Query: 18 IGSCGG--------MPWKISSDLKRFKSLTTGNPV-VMGYRTFQSIGRLLPGRTNIIITR 68
+G GG + D +F N V ++G QS G L P + R
Sbjct: 115 LGHTGGTLDKLESIPGVNLELDEIKFIEQVKDNGVAIIG----QS-GNLAPADKKLYALR 169
Query: 69 DNTRRASVNPEAVLASSILDSLDLASKTGSKKIFI---IGGG---EIYAQTISLAHTLY 121
D T A+V+ ++ASSI+ S LA+ G+ I + +G G + LA +
Sbjct: 170 DVT--ATVDSIPLIASSIM-SKKLAA--GADAIVLDVKVGSGAFMKTVEDARELAKAMV 223
>gnl|CDD|36395 KOG1180, KOG1180, KOG1180, Acyl-CoA synthetase [Lipid transport and
metabolism].
Length = 678
Score = 26.8 bits (59), Expect = 3.4
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 21 CGGMPWKISSDLKRFKSLTTGNPVVMGY 48
GG P +S D +RF ++ PV+ GY
Sbjct: 409 SGGAP--LSPDTQRFMNICFCCPVLQGY 434
>gnl|CDD|145065 pfam01715, IPPT, IPP transferase. This is a family of IPP
transferases EC:2.5.1.8 also known as tRNA
delta(2)-isopentenylpyrophosphate transferase. These
enzymes modify both cytoplasmic and mitochondrial tRNAs
at A(37) to give isopentenyl A(37).
Length = 253
Score = 26.5 bits (59), Expect = 3.6
Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 16/70 (22%)
Query: 91 DLASKTGSKKIFIIGGGEIYAQTISLAHTLYITHIEKEIEGDVFFPSIDSNIWKKQEKEI 150
+A KI ++ GG LY + ++G PS D + K E+++
Sbjct: 48 AIAEIRARGKIPLLVGGT----------GLYFKAL---LDGLSDTPSADPKVRAKLEEQL 94
Query: 151 ITSAGEGDDY 160
G+DY
Sbjct: 95 EE---LGNDY 101
>gnl|CDD|143445 cd07127, ALDH_PAD-PaaZ, Phenylacetic acid degradation proteins PaaZ
(Escherichia coli) and PaaN (Pseudomonas putida)-like.
Phenylacetic acid degradation (PAD) proteins PaaZ
(Escherichia coli) and PaaN (Pseudomonas putida) are
putative aromatic ring cleavage enzymes of the aerobic
PA catabolic pathway. PaaZ mutants were defective for
growth with PA as a sole carbon source due to
interruption of the putative ring opening system. This
CD is limited to bacterial monofunctional enzymes.
Length = 549
Score = 26.7 bits (59), Expect = 3.9
Identities = 15/30 (50%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 17 VIGSCGGMP-WKISSDLKRFKSLTTGNPVV 45
VIG C P W L F SL TGNPV+
Sbjct: 199 VIG-CSTFPTWNGYPGL--FASLATGNPVI 225
>gnl|CDD|33084 COG3273, COG3273, Uncharacterized conserved protein [Function
unknown].
Length = 204
Score = 26.4 bits (58), Expect = 4.6
Identities = 14/36 (38%), Positives = 17/36 (47%)
Query: 72 RRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGG 107
R V + LA L LDLA+ TG + I I G
Sbjct: 121 VRVRVEKGSELAGKTLGELDLATNTGVRVIAIRRGE 156
>gnl|CDD|146850 pfam04414, tRNA_deacylase, D-aminoacyl-tRNA deacylase. Several
aminoacyl-tRNA synthetases have the ability to transfer
the D-isomer of their amino acid onto their cognate
tRNA. D-aminoacyl-tRNA deacylases hydrolyse the ester
bond between the polynucleotide and the D-amino acid,
thereby preventing the accumulation of such mis-acylated
and metabolically inactive tRNA molecules.
Length = 214
Score = 26.5 bits (59), Expect = 4.7
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 76 VNPEAV--LASSILDSLDLASKTGSKKIFIIGGGEIYAQ---TISLAHTLYITHI 125
+P+A +A ++L++L + K IGGG YA I+L + HI
Sbjct: 106 NDPDAAEAVAEAVLEALGKDEEEEVKPAVGIGGGH-YAPRFTDIALETEYAVGHI 159
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(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 = 311
Score = 26.5 bits (59), Expect = 4.8
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 82 LASSILDSLDLASKTGSKKIFIIGGGEI 109
LA I +L KK+ +IG GE+
Sbjct: 168 LAEKIFGNL------KGKKVLVIGAGEM 189
>gnl|CDD|33705 COG3919, COG3919, Predicted ATP-grasp enzyme [General function
prediction only].
Length = 415
Score = 26.1 bits (57), Expect = 5.5
Identities = 7/26 (26%), Positives = 11/26 (42%)
Query: 90 LDLASKTGSKKIFIIGGGEIYAQTIS 115
D A K G K ++ G+ +S
Sbjct: 64 RDFAEKHGLKGYLLVACGDGEVLLVS 89
>gnl|CDD|145023 pfam01661, Macro, Macro domain. This domain is an ADP-ribose
binding module. It is found in a number of otherwise
unrelated proteins. It is found at the C-terminus of the
macro-H2A histone protein. This domain is found in the
non-structural proteins of several types of ssRNA
viruses such as NSP3 from alphaviruses. This domain is
also found on its own in a family of proteins from
bacteria, archaebacteria, and eukaryotes.
Length = 117
Score = 26.0 bits (58), Expect = 5.6
Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 12/84 (14%)
Query: 21 CGGMPWKISSDLKRFKSLTTGNPVV-MGYRTFQSIGRLLPGRTNIIITR--DNTRRASVN 77
G + +LK+ TG VV G LP + +I T
Sbjct: 22 AGPALLEECRELKKNGGCPTGEAVVTPGGN--------LPAK-YVIHTVGPIWRHGGGEE 72
Query: 78 PEAVLASSILDSLDLASKTGSKKI 101
E +LAS+ ++L+LA++ G K I
Sbjct: 73 EEELLASAYRNALELANELGIKSI 96
>gnl|CDD|31391 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 25.3 bits (55), Expect = 9.3
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 49 RTFQSIGRLLPGRTNIIITRDNTRR 73
R + + RL PG I I D TRR
Sbjct: 495 RIEEELKRLFPGARIIRIDSDTTRR 519
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
0.319 0.137 0.396
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,120,784
Number of extensions: 106072
Number of successful extensions: 234
Number of sequences better than 10.0: 1
Number of HSP's gapped: 224
Number of HSP's successfully gapped: 18
Length of query: 176
Length of database: 6,263,737
Length adjustment: 87
Effective length of query: 89
Effective length of database: 4,383,754
Effective search space: 390154106
Effective search space used: 390154106
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 (21.7 bits)
S2: 54 (24.5 bits)