Align Hydroxyacylglutathione hydrolase; EC 3.1.2.6; Glyoxalase II; Glx II (uncharacterized)
to candidate 3609305 Dshi_2691 Hydroxyacylglutathione hydrolase (RefSeq)
Query= curated2:A6WXE0 (260 letters) >FitnessBrowser__Dino:3609305 Length = 256 Score = 287 bits (735), Expect = 1e-82 Identities = 138/240 (57%), Positives = 170/240 (70%) Query: 19 NYGVLIHDPQSALTASIDAPDAAAIEAALKRRGWTLDFIFTTHHHLDHVEGNEALKAKYG 78 NYGVL+HDP S TAS+DA DAAA+ ALK+ GWTL I+ THHH DH +G +KA+ G Sbjct: 15 NYGVLLHDPSSGATASVDAGDAAALRTALKKTGWTLSEIWITHHHADHTDGVAEIKAETG 74 Query: 79 VSIIGPKAEETKIPGIDRTVKDGDEFTFGLFRVKVIATPGHTAGEVSYYLPDAKAVFTGD 138 ++IGPK + I G+D DGD F F V+VI TPGHT +++YLP VFTGD Sbjct: 75 CTVIGPKPQSAPIAGVDTRYGDGDRFDFSGHEVRVIHTPGHTIDMINFYLPAEGVVFTGD 134 Query: 139 TLFALGCGRLFEGTPLTMFQSLQKLVALPGDTAVYCGHEYTESNARFALTIDPANSALKE 198 TLF +GCGRLFEG M SLQKL ALP DT +YC HEYTE+NA FALT+DP N LK+ Sbjct: 135 TLFVMGCGRLFEGDGPMMHASLQKLAALPADTVIYCSHEYTEANADFALTVDPENPDLKD 194 Query: 199 RAAEIARLRAADRMTLPSSIALEMATNPFLRWHDAGIRSRLGLQDAPDEAVFAEIRKRKD 258 +AA + LRA D+ T+P+++A E+ATNPFLR HD IR+ LGL+ A D VF EIR+RKD Sbjct: 195 KAARVKALRAQDKPTVPTTLAEELATNPFLRAHDTRIRAHLGLETASDAEVFTEIRRRKD 254 Lambda K H 0.321 0.136 0.403 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 234 Number of extensions: 7 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 260 Length of database: 256 Length adjustment: 24 Effective length of query: 236 Effective length of database: 232 Effective search space: 54752 Effective search space used: 54752 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 (21.8 bits) S2: 47 (22.7 bits)
Align candidate 3609305 Dshi_2691 (Hydroxyacylglutathione hydrolase (RefSeq))
to HMM TIGR03413 (gloB: hydroxyacylglutathione hydrolase (EC 3.1.2.6))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR03413.hmm # target sequence database: /tmp/gapView.8275.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03413 [M=248] Accession: TIGR03413 Description: GSH_gloB: hydroxyacylglutathione hydrolase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-94 300.7 0.0 4.6e-94 300.4 0.0 1.0 1 lcl|FitnessBrowser__Dino:3609305 Dshi_2691 Hydroxyacylglutathione Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3609305 Dshi_2691 Hydroxyacylglutathione hydrolase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 300.4 0.0 4.6e-94 4.6e-94 10 247 .. 15 255 .. 13 256 .] 0.99 Alignments for each domain: == domain 1 score: 300.4 bits; conditional E-value: 4.6e-94 TIGR03413 10 Nyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfpvkvvgpaee..ripglt 83 Ny +ll+d++s +++ vD+g+a+ + +al+++g++l++i++THhHaDH++gvae++++++++v+gp+ + i+g++ lcl|FitnessBrowser__Dino:3609305 15 NYGVLLHDPSSgATASVDAGDAAALRTALKKTGWTLSEIWITHHHADHTDGVAEIKAETGCTVIGPKPQsaPIAGVD 91 9**********9******************************************************99877899*** PP TIGR03413 84 kevkegdevellelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtaeqmleslqklaaLpeetkv 160 ++ +gd++++ ++ev+v+++pGHt + i +yl++e+v+F+gDtLf +GCGrlfeg+ +m++slqklaaLp++t + lcl|FitnessBrowser__Dino:3609305 92 TRYGDGDRFDFSGHEVRVIHTPGHTIDMINFYLPAEGVVFTGDTLFVMGCGRLFEGDGPMMHASLQKLAALPADTVI 168 ***************************************************************************** PP TIGR03413 161 ycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraeeaevkaaleeekaeevev 237 yc+HEYt++N++Fal+v+pen++lk+++++v+alra++kpt+P+tlaee+atNpFLra++++++a+l+ e+a+++ev lcl|FitnessBrowser__Dino:3609305 169 YCSHEYTEANADFALTVDPENPDLKDKAARVKALRAQDKPTVPTTLAEELATNPFLRAHDTRIRAHLGLETASDAEV 245 ***************************************************************************** PP TIGR03413 238 faelRekkdk 247 f+e+R++kd+ lcl|FitnessBrowser__Dino:3609305 246 FTEIRRRKDN 255 *********7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (256 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.51 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory