Align Hydroxyacylglutathione hydrolase cytoplasmic; Glyoxalase II; Glx II; EC 3.1.2.6 (characterized)
to candidate AZOBR_RS20450 AZOBR_RS20450 hydroxyacylglutathione hydrolase
Query= SwissProt::O24496 (258 letters) >FitnessBrowser__azobra:AZOBR_RS20450 Length = 253 Score = 192 bits (487), Expect = 7e-54 Identities = 104/259 (40%), Positives = 145/259 (55%), Gaps = 9/259 (3%) Query: 1 MKIFHVPCLQDNYSYLIIDESTGDAAVVDPVDPEKVIASAEKHQAKIKFVLTTHHHWDHA 60 M I +P DNY YL+ D ++G VVDP D + V+A E+ + + THHH DH Sbjct: 1 MDIHLIPAFADNYIYLLRDPASGAVGVVDPGDAQPVLAELERRNWTLTHIFNTHHHNDHI 60 Query: 61 GGNEKIK-QLVPDIKVYGGSLDKVKGCTDAVDNGDKLTLGQDINILALHTPCHTKGHISY 119 GGN +K + D+ + ++ + G+ ++ G + P HT GHI++ Sbjct: 61 GGNHALKARYGADVIGPRADVARIPDMETCLGEGETISFGS-LAAQVFFVPGHTSGHIAF 119 Query: 120 YVNGKEGENPAVFTGDTLFVAGCGKFFEGTAEQMYQSLCVTLAALPKPTQVYCGHEYTVK 179 + E A+F GDTLF GCG+ FEGT QM+ SL V L LP T+VYCGHEYT+ Sbjct: 120 WFT----EAKALFCGDTLFALGCGRLFEGTPAQMWASL-VKLRGLPDDTRVYCGHEYTLS 174 Query: 180 NLEFALTVEPNNGKIQQKLAWARQQRQADLPTIPSTLEEELETNPFMRVDKPEIQEKLGC 239 N FA+TVEP+N ++ + A QR+ PTIPSTL E TNPF+R D PE+Q LG Sbjct: 175 NARFAVTVEPDNAALKARAADIAAQRERGEPTIPSTLGVEKATNPFLRADVPEVQSALGM 234 Query: 240 --KSPIDTMREVRNKKDQW 256 P+ E+R +KD++ Sbjct: 235 AGADPVAVFAEIRGRKDRF 253 Lambda K H 0.317 0.135 0.411 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: 193 Number of extensions: 11 Number of successful extensions: 4 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: 258 Length of database: 253 Length adjustment: 24 Effective length of query: 234 Effective length of database: 229 Effective search space: 53586 Effective search space used: 53586 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: 47 (22.7 bits)
Align candidate AZOBR_RS20450 AZOBR_RS20450 (hydroxyacylglutathione hydrolase)
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.26012.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-109 349.5 0.0 5.5e-109 349.3 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS20450 AZOBR_RS20450 hydroxyacylglutath Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS20450 AZOBR_RS20450 hydroxyacylglutathione hydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 349.3 0.0 5.5e-109 5.5e-109 1 248 [] 3 253 .] 3 253 .] 0.99 Alignments for each domain: == domain 1 score: 349.3 bits; conditional E-value: 5.5e-109 TIGR03413 1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp 68 i+ ipa++dNyi+ll+d++s ++ vvDpg+a+pvl+ le+++++l++i++THhH+DH+gg+++l+++++ lcl|FitnessBrowser__azobra:AZOBR_RS20450 3 IHLIPAFADNYIYLLRDPASgAVGVVDPGDAQPVLAELERRNWTLTHIFNTHHHNDHIGGNHALKARYG 71 688*****************9999********************************************* PP TIGR03413 69 vkvvgpaee..ripgltkevkegdevellelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGr 135 ++v+gp+++ rip +++ + eg+++++++l+++v+ vpGHt+gHia++++e+k+lFcgDtLf++GCGr lcl|FitnessBrowser__azobra:AZOBR_RS20450 72 ADVIGPRADvaRIPDMETCLGEGETISFGSLAAQVFFVPGHTSGHIAFWFTEAKALFCGDTLFALGCGR 140 *********99********************************************************** PP TIGR03413 136 lfegtaeqmleslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPs 204 lfegt++qm++sl kl+ Lp++t+vyc+HEYtlsN+rFa++vep+n+alk+r+++++a+r++g+pt+Ps lcl|FitnessBrowser__azobra:AZOBR_RS20450 141 LFEGTPAQMWASLVKLRGLPDDTRVYCGHEYTLSNARFAVTVEPDNAALKARAADIAAQRERGEPTIPS 209 ********************************************************************* PP TIGR03413 205 tlaeekatNpFLraeeaevkaaleeekaeevevfaelRekkdkf 248 tl+ ekatNpFLra+ +ev++al+++ a++v+vfae+R +kd+f lcl|FitnessBrowser__azobra:AZOBR_RS20450 210 TLGVEKATNPFLRADVPEVQSALGMAGADPVAVFAEIRGRKDRF 253 ******************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (253 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.20 // [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