RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780583|ref|YP_003064996.1| glyoxalase II [Candidatus
Liberibacter asiaticus str. psy62]
(256 letters)
>gnl|CDD|36031 KOG0813, KOG0813, KOG0813, Glyoxylase [General function prediction
only].
Length = 265
Score = 180 bits (458), Expect = 3e-46
Identities = 89/253 (35%), Positives = 127/253 (50%), Gaps = 9/253 (3%)
Query: 13 DNFCILIH-NHKYRLTAAID---APDTYIISKMLREKGWFLTHIFNTHHHIDHTRANLNL 68
DN+ L+ K +D K L ++ LT I THHH DH+ N ++
Sbjct: 12 DNYMYLLGDGDKTIDADLVDPAEPEYVIPSLKKLDDENRRLTAILTTHHHYDHSGGNEDI 71
Query: 69 KKFFNCTIFGPLEESSKIPGIDHGLSDGDTFDFGSHPIKIIATPGHTIGHICYHF---MN 125
K+ I +IPGI GL DG+T G ++ + TPGHT GHICY+
Sbjct: 72 KREIPYDIKVIGGADDRIPGITRGLKDGETVTVGGLEVRCLHTPGHTAGHICYYVTESTG 131
Query: 126 DHFLCVGDTLFSLGCGRIFEDSYAEMFESLEKIKSFSDKTHIYFGHEYTENNAYFALSCD 185
+ + GDTLF GCGR FE + +M SL ++ + D T IY GHEYT++N FA +
Sbjct: 132 ERAIFTGDTLFGAGCGRFFEGTAEQMDSSLNELIALPDDTRIYPGHEYTKSNLKFARYVE 191
Query: 186 PHNLELQKYCSKVKSMRSQNLYTN-PSTISLEKKVNPFLRIENTSLRKNLNM-ENASNLA 243
P N Q+ + RS+ T PST+ EK NPF+R++ ++K L + E A +
Sbjct: 192 PRNEVEQEKLDWLVERRSKEKPTMVPSTLGEEKLYNPFMRLKKEKVQKALGLTETADRIV 251
Query: 244 VFTELRIRKNQSK 256
V +LR KN+
Sbjct: 252 VMGKLRELKNRFS 264
>gnl|CDD|30837 COG0491, GloB, Zn-dependent hydrolases, including glyoxylases
[General function prediction only].
Length = 252
Score = 93.4 bits (230), Expect = 6e-20
Identities = 59/257 (22%), Positives = 92/257 (35%), Gaps = 49/257 (19%)
Query: 1 MTSLNIAISLYHDNFCILIHNHKYRLT---AAIDAPDTYIISKMLREKGWFLTHIFNTHH 57
+T+ I + N L+ + + + D + + L G + I TH
Sbjct: 12 ITAFPIGVGPLSGNSVYLLVDGEGGAVLIDTGLGDADAEALLEALAALGLDVDAILLTHG 71
Query: 58 HIDHTRANLNLKKFFNC-TIFGPLEESSKIPG-------------------IDHGLSDGD 97
H DH LK+ F + P E + L DGD
Sbjct: 72 HFDHIGGAAVLKEAFGAAPVIAPAEVPLLLREEILRKAGVTAEAYAAPGASPLRALEDGD 131
Query: 98 TFDFGSHPIKIIATPGHTIGHICYHFMNDHFLCVGDTLFS--LGCGR--IFEDSYAEMFE 153
D G ++++ TPGHT GHI + + L GDTLF+ G GR + A++
Sbjct: 132 ELDLGGLELEVLHTPGHTPGHIVFLLEDGGVLFTGDTLFAGDTGVGRLDLPGGDAAQLLA 191
Query: 154 SLEKIKSFS-DKTHIYFGH---EYTENNAYFALSCDPHNLELQKYCSKVKSMRSQNLYTN 209
SL ++ T + GH EY AL+ L
Sbjct: 192 SLRRLLLLLLPDTLVLPGHGPDEYDPAARALALTAPRL------------------LEVA 233
Query: 210 PSTISLEKKVNPFLRIE 226
+T+ E+++NPFLR+
Sbjct: 234 ETTLGDERRLNPFLRLF 250
>gnl|CDD|36032 KOG0814, KOG0814, KOG0814, Glyoxylase [General function prediction
only].
Length = 237
Score = 70.4 bits (172), Expect = 4e-13
Identities = 56/200 (28%), Positives = 83/200 (41%), Gaps = 12/200 (6%)
Query: 15 FCILIHNHKYRLTAAIDAPDTYII--SKMLREKGWFLTHIFNTHHHIDHTRANLNLKKFF 72
+ L+ +HK ID + ++++++ G L + NTH H DH LK
Sbjct: 22 YTYLLGDHKTGKAVIIDPVLETVSRDAQLIKDLGLDLIYALNTHVHADHITGTGLLKTLL 81
Query: 73 NCTIFGPLEESSKIPG--IDHGLSDGDTFDFGSHPIKIIATPGHTIGHICYHFMNDHFLC 130
G S G D L DGD + G +++ ATPGHT G + Y +
Sbjct: 82 P----GCKSVISSASGAKADLHLEDGDIIEIGGLKLEVRATPGHTNGCVTYVEHDLRMAF 137
Query: 131 VGDTLFSLGCGR--IFEDSYAEMFESL-EKIKSFSDKTHIYFGHEYTENNAYFALSCDPH 187
GD L GCGR + A ++ES+ KI + + IY H+Y
Sbjct: 138 TGDALLIRGCGRTDFQQGCPASLYESVHSKIFTLPEDYLIYPAHDYKGFLVSTVWEEKNL 197
Query: 188 NLELQKYCSK-VKSMRSQNL 206
N L K + VK M++ NL
Sbjct: 198 NPRLTKSKEEFVKIMKNLNL 217
>gnl|CDD|144377 pfam00753, Lactamase_B, Metallo-beta-lactamase superfamily.
Length = 148
Score = 62.4 bits (151), Expect = 1e-10
Identities = 27/126 (21%), Positives = 40/126 (31%), Gaps = 16/126 (12%)
Query: 28 AAIDAPDTYIISKMLREKGWFLTHIFNTHHHIDHTRANLNLKKFFNCTIFGPLEES---- 83
+ A D ++ L + I TH H DH LK+ + E++
Sbjct: 22 TGLGADDALLLLAALGLDPKDIDAIILTHAHADHIGGLPELKEATPAPVVAAPEDAAALL 81
Query: 84 ------------SKIPGIDHGLSDGDTFDFGSHPIKIIATPGHTIGHICYHFMNDHFLCV 131
+ D L GD G + + PGH GH+ + L
Sbjct: 82 RLGLDDAELRKLVDVLPPDVDLEGGDGILGGGTLLFVTPHPGHGPGHVVVYLPGGKVLFT 141
Query: 132 GDTLFS 137
GD LF
Sbjct: 142 GDLLFG 147
>gnl|CDD|30775 COG0426, FpaA, Uncharacterized flavoproteins [Energy production and
conversion].
Length = 388
Score = 33.7 bits (77), Expect = 0.047
Identities = 26/118 (22%), Positives = 41/118 (34%), Gaps = 9/118 (7%)
Query: 49 LTHIFNTHHHIDHTRA-NLNLKKFFNCTIFGP------LEESSKIPGIDHGLSDGDTFDF 101
+ +I H DH+ + L+ N I L+ P + GDT D
Sbjct: 73 IDYIIVNHTEPDHSGSLPELLELAPNAKIICSKLAARFLKGFYHDPEWFKIVKTGDTLDL 132
Query: 102 GSHPIKIIATPG-HTIGHICYHFMNDHFLCVGDTLFSLGCG-RIFEDSYAEMFESLEK 157
G H +K I P H + + D L D + C F++ E+ + K
Sbjct: 133 GGHTLKFIPAPFLHWPDTMFTYDPEDKILFSCDAFGAHVCDDYRFDEDIEELLPDMRK 190
>gnl|CDD|111553 pfam02667, SCFA_trans, Short chain fatty acid transporter. This
family consists of two sequences annotated as short
chain fatty acid transporters, however, there are no
references giving details of experimental
characterisation of this function.
Length = 453
Score = 30.6 bits (69), Expect = 0.48
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 102 GSHPIKIIATPGHTIGHICYHFMNDHFLCVGDTLFS 137
GS P+ + ATP + + HI + + +T+FS
Sbjct: 156 GSMPL-LAATPNNPLKHIFVELFGRETIPLNETIFS 190
>gnl|CDD|31519 COG1328, NrdD, Oxygen-sensitive ribonucleoside-triphosphate
reductase [Nucleotide transport and metabolism].
Length = 700
Score = 30.3 bits (68), Expect = 0.51
Identities = 16/89 (17%), Positives = 34/89 (38%), Gaps = 11/89 (12%)
Query: 145 EDSYAEMFESLEKIKSFSDKTHIYFGHEYT------ENNA-YFALSCDPHNLELQKYCSK 197
E++ + +E I+ ++DK G ++ E+ A FA ++
Sbjct: 507 EEAKKFGIKIVEYIREYADKWKKETGLRWSVYQTPAESLADRFARL----DIFEFGEYKV 562
Query: 198 VKSMRSQNLYTNPSTISLEKKVNPFLRIE 226
V+ + YTN + ++ V +I
Sbjct: 563 VRGDTDKPYYTNSFHVPVDADVTLGEKIR 591
>gnl|CDD|153084 cd01675, RNR_III, Class III ribonucleotide reductase.
Ribonucleotide reductase (RNR) catalyzes the reductive
synthesis of deoxyribonucleotides from their
corresponding ribonucleotides. It provides the
precursors necessary for DNA synthesis. RNRs are
separated into three classes based on their
metallocofactor usage. Class I RNRs, found in
eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in strict or facultative anaerobic bacteria,
bacteriophage, and archaea, use an FeS cluster and
S-adenosylmethionine to generate a glycyl radical. Many
organisms have more than one class of RNR present in
their genomes. All three RNRs have a ten-stranded
alpha-beta barrel domain that is structurally similar to
the domain of PFL (pyruvate formate lyase). The class
III enzyme from phage T4 consists of two subunits, this
model covers the larger subunit which contains the
active and allosteric sites.
Length = 555
Score = 28.8 bits (65), Expect = 1.5
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 9/75 (12%)
Query: 155 LEKIKSFSDKTHIYFGHEYT--ENNAY-FALSCDPHNLELQKYCSKVKSMRSQNLYTNPS 211
E+ F ++T + + E T E+ AY FA + +KY + + + YTN
Sbjct: 400 RERADEFKEETGLLYSVEATPAESLAYRFA------KKDRKKYGDIIPGVTDKPYYTNSF 453
Query: 212 TISLEKKVNPFLRIE 226
+ + + ++PF +I+
Sbjct: 454 HVPVYEDIDPFEKID 468
>gnl|CDD|146396 pfam03735, ENT, ENT domain. This presumed domain is named after
Emsy N Terminus (ENT). Emsy is a protein that is
amplified in breast cancer and interacts with BRCA2. The
N terminus of this protein is found to be similar to
other vertebrate and plant proteins of unknown function.
This domain has a completely conserved histidine residue
that may be functionally important.
Length = 74
Score = 28.0 bits (63), Expect = 2.5
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 11/57 (19%)
Query: 187 HNLELQKYCSKVKSMRSQNLYTNPSTISLEKKVNPFLRIENTSLRKNLNMENASNLA 243
H LEL+ Y + +++ R+Q +S EK+ L T LRK L + + +
Sbjct: 6 HRLELEAYAAVLRAFRAQG-----DALSWEKEE--LL----TELRKELRISDEEHRE 51
>gnl|CDD|133286 cd01886, EF-G, Elongation factor G (EF-G) subfamily. Translocation
is mediated by EF-G (also called translocase). The
structure of EF-G closely resembles that of the complex
between EF-Tu and tRNA. This is an example of molecular
mimicry; a protein domain evolved so that it mimics the
shape of a tRNA molecule. EF-G in the GTP form binds to
the ribosome, primarily through the interaction of its
EF-Tu-like domain with the 50S subunit. The binding of
EF-G to the ribosome in this manner stimulates the
GTPase activity of EF-G. On GTP hydrolysis, EF-G
undergoes a conformational change that forces its arm
deeper into the A site on the 30S subunit. To
accommodate this domain, the peptidyl-tRNA in the A site
moves to the P site, carrying the mRNA and the
deacylated tRNA with it. The ribosome may be prepared
for these rearrangements by the initial binding of EF-G
as well. The dissociation of EF-G leaves the ribosome
ready to accept the next aminoacyl-tRNA into the A site.
This group contains both eukaryotic and bacterial
members.
Length = 270
Score = 27.8 bits (63), Expect = 2.6
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 98 TFDFGSHPIKIIATPGH 114
T + H I II TPGH
Sbjct: 58 TCFWKDHRINIIDTPGH 74
>gnl|CDD|31428 COG1235, PhnP, Metal-dependent hydrolases of the beta-lactamase
superfamily I [General function prediction only].
Length = 269
Score = 27.4 bits (60), Expect = 4.4
Identities = 11/43 (25%), Positives = 19/43 (44%)
Query: 35 TYIISKMLREKGWFLTHIFNTHHHIDHTRANLNLKKFFNCTIF 77
+ + LR L I TH H DH + +L++ + I+
Sbjct: 49 PDLRDQGLRLGVSDLDAILLTHEHSDHIQGLDDLRRAYTLPIY 91
>gnl|CDD|38842 KOG3636, KOG3636, KOG3636, Uncharacterized conserved protein,
contains TBC and Rhodanese domains [General function
prediction only].
Length = 669
Score = 26.6 bits (58), Expect = 7.3
Identities = 27/100 (27%), Positives = 42/100 (42%), Gaps = 13/100 (13%)
Query: 132 GDTLFSLGCGRIFEDSYAEMFES--LEKIKSFSD-------KTHIYFGHEYTE----NNA 178
G+ L +G GR ED+Y M + L+K K + K H YFG + + +NA
Sbjct: 384 GEHLCFMGSGRDEEDNYMNMVIAMFLQKNKLYVSFVQGGYKKLHDYFGDQMADCIEDHNA 443
Query: 179 YFALSCDPHNLELQKYCSKVKSMRSQNLYTNPSTISLEKK 218
L C HN + K S S + + +++ K
Sbjct: 444 RKCLVCQQHNAQQTKSAPLKTSTPSSTDLFSKFSAAMKSK 483
>gnl|CDD|32402 COG2220, COG2220, Predicted Zn-dependent hydrolases of the
beta-lactamase fold [General function prediction only].
Length = 258
Score = 26.3 bits (57), Expect = 8.1
Identities = 21/110 (19%), Positives = 31/110 (28%), Gaps = 26/110 (23%)
Query: 49 LTHIFNTHHHIDHTRANLNLKKFFN--CTIFGPLEESSKIPGID--------HGLSDGDT 98
+ +I TH H DH + N + P + I H L GD
Sbjct: 53 IDYILITHDHYDHLDDETLIALRTNKAPVVVVP--LGAGDLLIRDGVEAERVHELGWGDV 110
Query: 99 FDFG--------SHPIKIIATPGHTI----GHICYHFMND--HFLCVGDT 134
+ G ++ + PG I + Y GDT
Sbjct: 111 IELGDLEITAVPAYHVSARHLPGRGIRPTGLWVGYVIETPGGRVYHAGDT 160
>gnl|CDD|31427 COG1234, ElaC, Metal-dependent hydrolases of the beta-lactamase
superfamily III [General function prediction only].
Length = 292
Score = 26.2 bits (57), Expect = 8.4
Identities = 7/13 (53%), Positives = 8/13 (61%)
Query: 49 LTHIFNTHHHIDH 61
+ IF TH H DH
Sbjct: 54 IDAIFITHLHGDH 66
>gnl|CDD|133430 cd05294, LDH-like_MDH_nadp, A lactate dehydrogenases-like structure
with malate dehydrogenase enzymatic activity. The
LDH-like MDH proteins have a lactate
dehyhydrogenase-like (LDH-like) structure and malate
dehydrogenase (MDH) enzymatic activity. This subgroup is
composed of some archaeal LDH-like MDHs that prefer
NADP(H) rather than NAD(H) as a cofactor. One member,
MJ0490 from Methanococcus jannaschii, has been observed
to form dimers and tetramers during crystalization,
although it is believed to exist primarilly as a
tetramer in solution. In addition to its MDH activity,
MJ0490 also possesses
fructose-1,6-bisphosphate-activated LDH activity.
Members of this subgroup have a higher sequence
similarity to LDHs than to other MDHs. LDH catalyzes the
last step of glycolysis in which pyruvate is converted
to L-lactate. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate. The
LDH-like MDHs are part of the NAD(P)-binding Rossmann
fold superfamily, which includes a wide variety of
protein families including the NAD(P)- binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenase,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 309
Score = 26.2 bits (58), Expect = 8.5
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 23 KYRLTAAIDAPDTYII----------SKMLREKGWFLTHIFNTHHHIDHTRANLNLKKFF 72
KY A APDT I+ K L+E G+ +F H+D R + + K F
Sbjct: 103 KYAKQIAEFAPDTKILVVTNPVDVMTYKALKESGFDKNRVFGLGTHLDSLRFKVAIAKHF 162
Query: 73 N 73
N
Sbjct: 163 N 163
>gnl|CDD|133434 cd05298, GH4_GlvA_pagL_like, Glycoside Hydrolases Family 4; GlvA-
and pagL-like glycosidases. Bacillus subtilis GlvA and
Clostridium acetobutylicum pagL are
6-phospho-alpha-glucosidase, catalyzing the hydrolysis
of alpha-glucopyranoside bonds to release glucose from
oligosaccharides. The substrate specificities of other
members of this subgroup are unknown. Some bacteria
simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP_PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by the GH4 glycoside hydrolases, which
include 6-phospho-beta-glucosidases,
6-phospho-alpha-glucosidases,
alpha-glucosidases/alpha-glucuronidases (only from
Thermotoga), and alpha-galactosidases. Members of this
subfamily are part of the NAD(P)-binding Rossmann fold
superfamily, which includes a wide variety of protein
families including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 437
Score = 26.1 bits (58), Expect = 8.8
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 14/58 (24%)
Query: 56 HHHIDHTRANLNL----KKFFNCTIFGPLEESSKIPGIDHGLSDGDTFDFGSHPIKII 109
H + ++TRAN + K+ F EE KI I+ G ++G TF H I+
Sbjct: 273 HSNPNYTRANEVMDGREKRVF--------EECRKI--IETGTAEGSTFHVDVHGEYIV 320
>gnl|CDD|146543 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 26.0 bits (58), Expect = 8.9
Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 185 DPHNL-ELQKYCSKVKSMRSQ 204
+ L EL+K KVK + S
Sbjct: 10 TFYTLKELEKLAPKVKGISSM 30
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
0.323 0.137 0.422
Gapped
Lambda K H
0.267 0.0716 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,143,677
Number of extensions: 165359
Number of successful extensions: 415
Number of sequences better than 10.0: 1
Number of HSP's gapped: 408
Number of HSP's successfully gapped: 21
Length of query: 256
Length of database: 6,263,737
Length adjustment: 92
Effective length of query: 164
Effective length of database: 4,275,709
Effective search space: 701216276
Effective search space used: 701216276
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 (22.0 bits)
S2: 56 (25.4 bits)