Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate 6937743 Sama_1884 hydroxyacylglutathione hydrolase (RefSeq)
Query= CharProtDB::CH_024825 (251 letters) >FitnessBrowser__SB2B:6937743 Length = 258 Score = 213 bits (541), Expect = 4e-60 Identities = 116/259 (44%), Positives = 157/259 (60%), Gaps = 10/259 (3%) Query: 1 MNLNSIPAFDDNYIWVLNDEAGRCLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHVG 60 +++ IPAF DNYIW++ G ++VDPGDA PV+N + N Q A+ LTHHH DH G Sbjct: 2 LDIRPIPAFADNYIWMIVLPDGGAVVVDPGDAMPVINTLQRLNLQLTAVLLTHHHRDHNG 61 Query: 61 GVKELVE----KFPQIVVYGPQETQDKGTTQVVKDGETAFVLG--HEFSVIATPGHTLGH 114 G+ +L + VYG T D + +DG+T + G V++ PGHTL H Sbjct: 62 GINQLRDWAKSNGQSFTVYGAV-TSDYSDV-LCRDGDTVDISGLTSPVRVLSVPGHTLDH 119 Query: 115 ICYFSKPYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKF 174 + + LFCGDTLFSGGCGRLFEG A Q+Y SL KL++LPDDTLV CAHEYTLSN++F Sbjct: 120 LAFVVDNALFCGDTLFSGGCGRLFEGDAGQLYDSLAKLASLPDDTLVYCAHEYTLSNLRF 179 Query: 175 ALSILPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEETLL 234 AL++ P + + DY ++V LR N+ +LP L E+ IN FLR + + + + Sbjct: 180 ALAVEPQNQCLQDYVKQVNNLREANKPSLPSTLGTEKAINPFLRVDTATVHAAVAAQAGQ 239 Query: 235 QQPEE--RFAWLRSKKDRF 251 + P+E A LR KD F Sbjct: 240 KVPDEVTCLALLRRWKDNF 258 Lambda K H 0.321 0.138 0.425 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: 243 Number of extensions: 15 Number of successful extensions: 2 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: 258 Length adjustment: 24 Effective length of query: 227 Effective length of database: 234 Effective search space: 53118 Effective search space used: 53118 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 6937743 Sama_1884 (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.2342504.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-96 308.0 0.0 2.5e-96 307.8 0.0 1.0 1 FitnessBrowser__SB2B:6937743 Domain annotation for each sequence (and alignments): >> FitnessBrowser__SB2B:6937743 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 307.8 0.0 2.5e-96 2.5e-96 1 248 [] 4 258 .] 4 258 .] 0.94 Alignments for each domain: == domain 1 score: 307.8 bits; conditional E-value: 2.5e-96 TIGR03413 1 iiaipalsdNyiwllkdekseavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp.....vkvvgpae 76 i +ipa++dNyiw++ ++ avvvDpg+a pv+++l++ +l+l+a+llTHhH+DH gg+++l++ ++ +v+g+ + FitnessBrowser__SB2B:6937743 4 IRPIPAFADNYIWMIVLPDGGAVVVDPGDAMPVINTLQRLNLQLTAVLLTHHHRDHNGGINQLRDWAKsngqsFTVYGAVT 84 679************************************************************875443345689999987 PP TIGR03413 77 eripgltkevkegdevel..lelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtaeqmleslqklaaLp 155 ++ ++ ++gd+v++ l++ v+vl+vpGHtl+H+a++++ ++lFcgDtLfs GCGrlfeg+a q+++sl kla+Lp FitnessBrowser__SB2B:6937743 85 SDY--SDVLCRDGDTVDIsgLTSPVRVLSVPGHTLDHLAFVVD--NALFCGDTLFSGGCGRLFEGDAGQLYDSLAKLASLP 161 655..57999*******97778889******************..9*********************************** PP TIGR03413 156 eetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraeeaevkaalee....eka 232 ++t+vycaHEYtlsNlrFalavep+n+ l++++k+v++lr+++kp+lPstl++eka+NpFLr+++a+v+aa+++ + FitnessBrowser__SB2B:6937743 162 DDTLVYCAHEYTLSNLRFALAVEPQNQCLQDYVKQVNNLREANKPSLPSTLGTEKAINPFLRVDTATVHAAVAAqagqKVP 242 ********************************************************************9999887887888 PP TIGR03413 233 eevevfaelRekkdkf 248 +ev+++a lR++kd+f FitnessBrowser__SB2B:6937743 243 DEVTCLALLRRWKDNF 258 99************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (258 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: 13.05 // [ok]
This GapMind analysis is from Apr 09 2024. 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