Align hydroxyacylglutathione hydrolase (EC 3.1.2.6) (characterized)
to candidate Ac3H11_478 Hydroxyacylglutathione hydrolase (EC 3.1.2.6)
Query= BRENDA::Q8ZRM2 (251 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_478 Length = 261 Score = 206 bits (523), Expect = 5e-58 Identities = 108/226 (47%), Positives = 147/226 (65%), Gaps = 10/226 (4%) Query: 1 MNLNSIPAFQDNYIWVLTNDEGRCVIVDPGEAAPVLKAIAEHKWMPEAIFLTHHHHDHVG 60 MNL +PAF DNYIW+L +D + ++VDPG+AAPV++A+ +AI +THHH DHVG Sbjct: 1 MNLLPLPAFTDNYIWML-HDGRQAIVVDPGDAAPVVQALDTLGLGLQAILVTHHHADHVG 59 Query: 61 GVKELLQHFPQMTVYGPAETQDKGATHLVGDGDTIR---VLGEKFTLFATPGHTLGHVCY 117 GV + L+ VYGPA + + GD + VLG +FT+ PGHT GH+ Y Sbjct: 60 GV-DTLREATGARVYGPARERIPEPLVRLAQGDVVEGADVLGLRFTVIDVPGHTAGHIAY 118 Query: 118 FSR-----PYLFCGDTLFSGGCGRLFEGTPSQMYQSLMKINSLPDDTLICCAHEYTLANI 172 + P LFCGDTLFSGGCGRLFEGTP+QM SL ++ +LP +T +CC HEYTL+N+ Sbjct: 119 YCEAMDGAPLLFCGDTLFSGGCGRLFEGTPAQMLDSLDQLAALPGNTRVCCTHEYTLSNL 178 Query: 173 KFALSILPHDSFINEYYRKVKELRVKKQMTLPVILKNERKINLFLR 218 KFA ++ P ++ + Y + + LR ++Q TLP + ER IN FLR Sbjct: 179 KFARAVEPGNAALLHYSSQCEALRAQQQPTLPSRMDLERDINPFLR 224 Lambda K H 0.323 0.140 0.436 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: 239 Number of extensions: 15 Number of successful extensions: 6 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: 251 Length of database: 261 Length adjustment: 24 Effective length of query: 227 Effective length of database: 237 Effective search space: 53799 Effective search space used: 53799 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
Align candidate Ac3H11_478 (Hydroxyacylglutathione hydrolase (EC 3.1.2.6))
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.1264.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-103 330.6 0.0 3.1e-103 330.4 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_478 Hydroxyacylglutathione hydrolase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_478 Hydroxyacylglutathione hydrolase (EC 3.1.2.6) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 330.4 0.0 3.1e-103 3.1e-103 3 248 .] 5 260 .. 3 260 .. 0.96 Alignments for each domain: == domain 1 score: 330.4 bits; conditional E-value: 3.1e-103 TIGR03413 3 aipalsdNyiwllkdekseavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaelle 65 ++pa++dNyiw+l+d + +a+vvDpg+a+pv++al++ gl l+ail+THhHaDHvggv++l+e lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_478 5 PLPAFTDNYIWMLHDGR-QAIVVDPGDAAPVVQALDTLGLGLQAILVTHHHADHVGGVDTLRE 66 79**************9.********************************************* PP TIGR03413 66 kfpvkvvgpaeeripgltkevkegdevel...lelevevlevpGHtlgHiayyleee...kvl 122 +++++v+gpa+erip+ +++++gd ve l+l+++v++vpGHt+gHiayy+e+ ++l lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_478 67 ATGARVYGPARERIPEPLVRLAQGDVVEGadvLGLRFTVIDVPGHTAGHIAYYCEAMdgaPLL 129 *************************9975444999*******************9878889** PP TIGR03413 123 FcgDtLfsaGCGrlfegtaeqmleslqklaaLpeetkvycaHEYtlsNlrFalavepenealk 185 FcgDtLfs GCGrlfegt++qml+sl++laaLp +t+v+c+HEYtlsNl+Fa+avep n+al lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_478 130 FCGDTLFSGGCGRLFEGTPAQMLDSLDQLAALPGNTRVCCTHEYTLSNLKFARAVEPGNAALL 192 *************************************************************** PP TIGR03413 186 erlkevealrakgkptlPstlaeekatNpFLraeeaevkaalee.....ekaeevevfaelRe 243 ++ +++ealra+++ptlPs+++ e+++NpFLr+++++v++a++ ++++v+v+a+lR+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_478 193 HYSSQCEALRAQQQPTLPSRMDLERDINPFLRVRQPTVAQAARGhdaqvPENDAVAVLAALRQ 255 **************************************998877788888999********** PP TIGR03413 244 kkdkf 248 +k++f lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_478 256 WKNEF 260 ***98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (261 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.69 // [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