RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1579
(258 letters)
>gnl|CDD|238127 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 = 139 bits (352), Expect = 2e-41
Identities = 56/195 (28%), Positives = 92/195 (47%), Gaps = 62/195 (31%)
Query: 25 KDMAHFSRITKKTENSNRVNAVIMGRKTWDSIPEKFRPLPGRYNVVLTRNSDLGSQLTGP 84
+D+ HF + T N VIMGRKT++SIP RPLPGR N+VL+R D
Sbjct: 25 EDLKHFKKTTTG-------NPVIMGRKTFESIPR--RPLPGRTNIVLSRQLDYQD---AE 72
Query: 85 NVTTTSSLDQAIDLLRHKKSKGEIENVWVIGGSSIYKLTEPLMNRLSTFPKKKGLILLCT 144
V SL++A++L + +E ++VIGG+ IYK
Sbjct: 73 GVEVVHSLEEALELAENT-----VEEIFVIGGAEIYKQ---------------------- 105
Query: 145 RKSNASFMFSVLSLQESLNSPYCDKVYVTQIHHHFDCDTFFPSLS-DKFQLIKDPNIPDD 203
+ PY D++Y+T+IH F+ DTFFP + +++L+ ++
Sbjct: 106 ------AL------------PYADRLYLTRIHAEFEGDTFFPEIDESEWELVS----EEE 143
Query: 204 VQKENDLNFQFKVFQ 218
V +E+ ++ F+ ++
Sbjct: 144 VFEEDGYSYTFETYE 158
>gnl|CDD|215777 pfam00186, DHFR_1, Dihydrofolate reductase.
Length = 159
Score = 132 bits (335), Expect = 8e-39
Identities = 54/195 (27%), Positives = 87/195 (44%), Gaps = 63/195 (32%)
Query: 26 DMAHFSRITKKTENSNRVNAVIMGRKTWDSIPEKFRPLPGRYNVVLTRNSDLGSQLTGPN 85
D+ HF +T +IMGRKT++SI RPLPGR N+VLTRN D +
Sbjct: 27 DLKHFKALTMG-------KPIIMGRKTFESIG---RPLPGRTNIVLTRNPDFKA----EG 72
Query: 86 VTTTSSLDQAIDLLRHKKSKGEIENVWVIGGSSIYKLTEPLMNRLSTFPKKKGLILLCTR 145
V SL++A+ L + E +++IGG+ IYK
Sbjct: 73 VEVVHSLEEALALAAGE------EEIFIIGGAEIYKQ----------------------- 103
Query: 146 KSNASFMFSVLSLQESLNSPYCDKVYVTQIHHHFDCDTFFPSLS-DKFQLIKDPNIPDDV 204
+ PY D++Y+T+I F+ DTFFP + +++L+ P D
Sbjct: 104 -----AL------------PYADRLYLTEIDAEFEGDTFFPEIDLSEWELVSREEHPKD- 145
Query: 205 QKENDLNFQFKVFQK 219
++N ++ F +++
Sbjct: 146 -EKNPYDYTFVTYER 159
>gnl|CDD|240299 PTZ00164, PTZ00164, bifunctional dihydrofolate
reductase-thymidylate synthase; Provisional.
Length = 514
Score = 122 bits (307), Expect = 7e-32
Identities = 62/201 (30%), Positives = 96/201 (47%), Gaps = 52/201 (25%)
Query: 26 DMAHFSRITKKTENSN------RVNAVIMGRKTWDSIPEKFRPLPGRYNVVLTRNSDLGS 79
DM FS+IT + NAVIMGRKTW+SIP+KFRPL R NVVL+R L
Sbjct: 35 DMKFFSKITTYVREEKYEKSPKKQNAVIMGRKTWESIPKKFRPLKNRINVVLSRT--LTE 92
Query: 80 QLTGPNVTTTSSLDQAIDLLRHKKSKGEIENVWVIGGSSIYKLTEPLMNRLSTFPKKKGL 139
+ P V SL+ A+ LL S IE +++IGG+S+Y+
Sbjct: 93 EEADPGVLVFGSLEDALRLLAEDLS---IEKIFIIGGASVYR------------------ 131
Query: 140 ILLCTRKSNASFMFSVLSLQESLNSPYCDKVYVTQIHHHFDCDTFFPSLSDKFQLIKDPN 199
E+L++ DK+Y+T+++ ++CD FFP + + F ++
Sbjct: 132 --------------------EALSANLLDKIYLTRVNSEYECDVFFPKIPESFFIV---A 168
Query: 200 IPDDVQKENDLNFQFKVFQKE 220
I N ++ F +++K+
Sbjct: 169 IVSQTFSTNGTSYDFVIYEKK 189
>gnl|CDD|223340 COG0262, FolA, Dihydrofolate reductase [Coenzyme metabolism].
Length = 167
Score = 95.1 bits (237), Expect = 3e-24
Identities = 46/164 (28%), Positives = 72/164 (43%), Gaps = 53/164 (32%)
Query: 26 DMAHFSRITKKTENSNRVNAVIMGRKTWDSIPEKFRPLPGRYNVVLTRNSDLGSQLTGPN 85
D+AHF T VIMGRKT++S+P ++RPLPGR N+VL+RN DL + G
Sbjct: 27 DLAHFKATTLG-------KPVIMGRKTYESLPGEWRPLPGRKNIVLSRNPDL--KTEG-G 76
Query: 86 VTTTSSLDQAIDLLRHKKSKGEIENVWVIGGSSIYKLTEPLMNRLSTFPKKKGLILLCTR 145
V S+++A+ LL ++ E++++IGG +Y+
Sbjct: 77 VEVVDSIEEALLLLLKEEG----EDIFIIGGGELYRQF---------------------- 110
Query: 146 KSNASFMFSVLSLQESLNSPYCDKVYVTQIHHHF-DCDTFFPSL 188
L + D++ +T I + DT FP
Sbjct: 111 ----------------LPAGLADELILTIIPVLLGEGDTLFPEG 138
>gnl|CDD|182714 PRK10769, folA, dihydrofolate reductase; Provisional.
Length = 159
Score = 70.5 bits (173), Expect = 3e-15
Identities = 38/106 (35%), Positives = 53/106 (50%), Gaps = 23/106 (21%)
Query: 26 DMAHFSRITKKTENSNRVN-AVIMGRKTWDSIPEKFRPLPGRYNVVLTRNSDLGSQLTGP 84
D+A F R N +N VIMGR TW+SI RPLPGR N+V++ T
Sbjct: 27 DLAWFKR--------NTLNKPVIMGRHTWESIG---RPLPGRKNIVISSQPG-----TDD 70
Query: 85 NVTTTSSLDQAIDLLRHKKSKGEIENVWVIGGSSIYKLTEPLMNRL 130
VT S+D+A+ + G++ + VIGG +Y+ P RL
Sbjct: 71 RVTWVKSVDEAL------AAAGDVPEIMVIGGGRVYEQFLPKAQRL 110
>gnl|CDD|219631 pfam07902, Gp58, gp58-like protein. Sequences found in this family
are derived from a number of bacteriophage and prophage
proteins. They are similar to gp58, a minor structural
protein of Lactococcus delbrueckii bacteriophage LL-H.
Length = 601
Score = 33.4 bits (76), Expect = 0.12
Identities = 24/82 (29%), Positives = 39/82 (47%)
Query: 38 ENSNRVNAVIMGRKTWDSIPEKFRPLPGRYNVVLTRNSDLGSQLTGPNVTTTSSLDQAID 97
E SNR AV ++T DS + + Y+ + + L S ++GPN S Q
Sbjct: 262 EISNREGAVSRVQQTLDSYQRRLQDAEDNYSSLTQTVAGLQSTVSGPNSKIQSRFTQLAG 321
Query: 98 LLRHKKSKGEIENVWVIGGSSI 119
L+ K ++G +E++ G SI
Sbjct: 322 LIDQKVTRGGVESIISQSGDSI 343
>gnl|CDD|223759 COG0687, PotD, Spermidine/putrescine-binding periplasmic protein
[Amino acid transport and metabolism].
Length = 363
Score = 31.6 bits (72), Expect = 0.34
Identities = 23/76 (30%), Positives = 32/76 (42%), Gaps = 11/76 (14%)
Query: 51 KTWDSI--PEKFRPLPGRYNVVLTRNSD-LGSQLT----GPNVTTTSSLDQAIDLLRHKK 103
+W + PEKF L G+ +L + + G+ L PN T L +A DLL K
Sbjct: 155 TSWADLFDPEKFPGLKGKGVALLDDDREVFGAALALLGKSPNTTDPEDLKKAFDLLDKLK 214
Query: 104 SKGEIENVWVIGGSSI 119
NV+ GS
Sbjct: 215 P----VNVYWFDGSQY 226
>gnl|CDD|205445 pfam13265, DUF4056, Protein of unknown function (DUF4056). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 355 and 380 amino
acids in length.
Length = 271
Score = 30.7 bits (70), Expect = 0.69
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 12/36 (33%)
Query: 53 WDS---IPEKFRPLPGRYNVVLTRNSDLGSQLTGPN 85
WDS +P+KF +VL R+ LG PN
Sbjct: 240 WDSSRRVPDKF--------LVLKRDYHLGDDRL-PN 266
>gnl|CDD|176207 cd08245, CAD, Cinnamyl alcohol dehydrogenases (CAD) and related
proteins. Cinnamyl alcohol dehydrogenases (CAD),
members of the medium chain dehydrogenase/reductase
family, reduce cinnamaldehydes to cinnamyl alcohols in
the last step of monolignal metabolism in plant cells
walls. CAD binds 2 zinc ions and is NADPH- dependent.
CAD family members are also found in non-plant species,
e.g. in yeast where they have an aldehyde reductase
activity. The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes, or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 330
Score = 29.2 bits (66), Expect = 2.1
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 5/61 (8%)
Query: 49 GRKTWDSIPEKFRPLPGRYNVVLTRNSDLGSQLTGPNVTTTSSLDQAIDLLRHKKSKGEI 108
GR +PE P + +++ R S GS G + L +A+D K K I
Sbjct: 250 GRIVLVGLPESPPFSPDIFPLIMKRQSIAGSTHGGR-----ADLQEALDFAAEGKVKPMI 304
Query: 109 E 109
E
Sbjct: 305 E 305
>gnl|CDD|223840 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 475
Score = 29.2 bits (66), Expect = 2.4
Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 20/66 (30%)
Query: 58 EKFRPLPGRYNVVLTRNSDLGSQLTGPNVT-----TTSSLDQAIDLLR-HKKSKGEIENV 111
E +P+PGR +V + G V L++A+ +R H + +
Sbjct: 316 ETLKPVPGRMELV---------NIGGKLVIVDYAHNPDGLEKALRAVRLHAAGR-----L 361
Query: 112 WVIGGS 117
V+ G
Sbjct: 362 IVVFGC 367
>gnl|CDD|163426 TIGR03714, secA2, accessory Sec system translocase SecA2. Members
of this protein family are homologous to SecA and part
of the accessory Sec system. This system, including both
five core proteins for export and a variable number of
proteins for glycosylation, operates in certain
Gram-positive pathogens for the maturation and delivery
of serine-rich glycoproteins such as the cell surface
glycoprotein GspB in Streptococcus gordonii [Protein
fate, Protein and peptide secretion and trafficking].
Length = 762
Score = 29.2 bits (66), Expect = 2.4
Identities = 15/52 (28%), Positives = 25/52 (48%)
Query: 192 FQLIKDPNIPDDVQKENDLNFQFKVFQKELAPKPHSLNVWNHKNYNFRVTVI 243
+Q DP+ D KE +F ++ KEL+ K LN N R++++
Sbjct: 660 YQFKNDPDEFDLKNKEAIKDFLKEIADKELSEKKKVLNNDYLFNDFERLSIL 711
>gnl|CDD|130262 TIGR01194, cyc_pep_trnsptr, cyclic peptide transporter. This model
describes cyclic peptide transporter in bacteria.
Bacteria have elaborate pathways for the production of
toxins and secondary metabolites. Many such compounds,
including syringomycin and pyoverdine are synthesized on
non-ribosomal templates consisting of a multienzyme
complex. On several occasions the proteins of the
complex and transporter protein are present on the same
operon. Often times these compounds cross the biological
membrane by specific transporters. Syringomycin is an
amphipathic, cylclic lipodepsipeptide when inserted into
host causes formation of channels, permeable to variety
of cations. On the other hand, pyoverdine is a cyclic
octa-peptidyl dihydroxyquinoline, which is efficient in
sequestering iron for uptake [Transport and binding
proteins, Amino acids, peptides and amines, Transport
and binding proteins, Other].
Length = 555
Score = 28.4 bits (63), Expect = 4.1
Identities = 13/48 (27%), Positives = 19/48 (39%)
Query: 62 PLPGRYNVVLTRNSDLGSQLTGPNVTTTSSLDQAIDLLRHKKSKGEIE 109
P+ + + R +D G + P S + LL H KS IE
Sbjct: 292 PILAQAQIACQRLADFGERFNEPEPELELSDADNVLLLAHDKSVDSIE 339
>gnl|CDD|169400 PRK08356, PRK08356, hypothetical protein; Provisional.
Length = 195
Score = 27.1 bits (60), Expect = 9.2
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 8/39 (20%)
Query: 95 AIDLLRHKK--------SKGEIENVWVIGGSSIYKLTEP 125
A+D R+ K S+GE+E + +GG IY +P
Sbjct: 87 AVDKKRNCKNIAIDGVRSRGEVEAIKRMGGKVIYVEAKP 125
>gnl|CDD|185126 PRK15204, PRK15204, undecaprenyl-phosphate galactose
phosphotransferase; Provisional.
Length = 476
Score = 27.3 bits (60), Expect = 9.6
Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 23/96 (23%)
Query: 122 LTEPLMNRLSTFPKKKGLILLCTRKSNASFMFSVLSLQESLNSPYCDKVYVTQIHHHFDC 181
LT+ L+N+L + KKK +IL NA +S L +E + FD
Sbjct: 134 LTKHLLNKLGIW-KKKTIIL--GSGQNARGAYSALQSEEMMG---------------FDV 175
Query: 182 DTFFPSLSDKFQL-----IKDPNIPDDVQKENDLNF 212
FF + + ++ IKD I D+ + D+++
Sbjct: 176 IAFFDTDASDAEINMLPVIKDTEIIWDLNRTGDVHY 211
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
0.322 0.136 0.414
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,720,142
Number of extensions: 1150906
Number of successful extensions: 999
Number of sequences better than 10.0: 1
Number of HSP's gapped: 986
Number of HSP's successfully gapped: 24
Length of query: 258
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 163
Effective length of database: 6,723,972
Effective search space: 1096007436
Effective search space used: 1096007436
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: 58 (26.1 bits)