Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate BWI76_RS05440 BWI76_RS05440 hydroxyacylglutathione hydrolase
Query= CharProtDB::CH_024825 (251 letters) >FitnessBrowser__Koxy:BWI76_RS05440 Length = 251 Score = 409 bits (1052), Expect = e-119 Identities = 192/251 (76%), Positives = 215/251 (85%) Query: 1 MNLNSIPAFDDNYIWVLNDEAGRCLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHVG 60 MNL SIPAF DNYIWVL++++GRCLIVDPG+A PVL AI N WQPEAI LTHHHHDHV Sbjct: 1 MNLISIPAFQDNYIWVLSEDSGRCLIVDPGEAAPVLAAIEQNRWQPEAILLTHHHHDHVD 60 Query: 61 GVKELVEKFPQIVVYGPQETQDKGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYFSK 120 GVK+L EKFP I VYGP ETQDKG T +VKDGE+ VLG EFS+ ATPGHTLGHIC+FS Sbjct: 61 GVKKLREKFPAIAVYGPAETQDKGITHIVKDGESISVLGREFSIFATPGHTLGHICFFSA 120 Query: 121 PYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKFALSILP 180 PYLFCGDT+FSGGCGRLFEG A QMYQS KK++ALPD+TL+CCAHEYTL+NMKFA+SILP Sbjct: 121 PYLFCGDTMFSGGCGRLFEGNAEQMYQSFKKINALPDETLICCAHEYTLANMKFAMSILP 180 Query: 181 HDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEETLLQQPEER 240 HD INDYY KV ELRAKNQ TLPVILKNER+IN+FLRT+D DLI I++ET LQ +R Sbjct: 181 HDRDINDYYHKVNELRAKNQKTLPVILKNERRINLFLRTDDDDLIKEISKETNLQHSAQR 240 Query: 241 FAWLRSKKDRF 251 FAWLRSKKD F Sbjct: 241 FAWLRSKKDDF 251 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: 306 Number of extensions: 4 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: 251 Length of database: 251 Length adjustment: 24 Effective length of query: 227 Effective length of database: 227 Effective search space: 51529 Effective search space used: 51529 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: 46 (22.3 bits)
Align candidate BWI76_RS05440 BWI76_RS05440 (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.5819.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-107 344.1 0.0 2.4e-107 343.9 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS05440 BWI76_RS05440 hydroxyacylglutath Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS05440 BWI76_RS05440 hydroxyacylglutathione hydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 343.9 0.0 2.4e-107 2.4e-107 2 248 .] 4 251 .] 3 251 .] 0.99 Alignments for each domain: == domain 1 score: 343.9 bits; conditional E-value: 2.4e-107 TIGR03413 2 iaipalsdNyiwllkdekseavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp.vkv 71 i+ipa++dNyiw+l++++ ++++vDpgea+pvl+a+e++++++eaillTHhH+DHv+gv++l+ekfp ++v lcl|FitnessBrowser__Koxy:BWI76_RS05440 4 ISIPAFQDNYIWVLSEDSGRCLIVDPGEAAPVLAAIEQNRWQPEAILLTHHHHDHVDGVKKLREKFPaIAV 74 78********************************************************************* PP TIGR03413 72 vgpaeeripgltkevkegdevellelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtae 142 +gpae++ +g+t+ vk+g+++++l++e++++++pGHtlgHi+++++ ++lFcgDt+fs GCGrlfeg+ae lcl|FitnessBrowser__Koxy:BWI76_RS05440 75 YGPAETQDKGITHIVKDGESISVLGREFSIFATPGHTLGHICFFSA--PYLFCGDTMFSGGCGRLFEGNAE 143 **********************************************..*********************** PP TIGR03413 143 qmleslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatN 213 qm++s++k++aLp+et+++caHEYtl+N++Fa+++ p+++++++++++v++lrak++ tlP+ l++e+++N lcl|FitnessBrowser__Koxy:BWI76_RS05440 144 QMYQSFKKINALPDETLICCAHEYTLANMKFAMSILPHDRDINDYYHKVNELRAKNQKTLPVILKNERRIN 214 *********************************************************************** PP TIGR03413 214 pFLraeeaevkaalee..ekaeevevfaelRekkdkf 248 +FLr+++ ++ +++++ + +++++ fa lR+kkd+f lcl|FitnessBrowser__Koxy:BWI76_RS05440 215 LFLRTDDDDLIKEISKetNLQHSAQRFAWLRSKKDDF 251 ************999977888999***********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (251 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.20 // [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