Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate BPHYT_RS15260 BPHYT_RS15260 chorismate mutase
Query= BRENDA::Q2SY64 (202 letters) >FitnessBrowser__BFirm:BPHYT_RS15260 Length = 198 Score = 266 bits (680), Expect = 2e-76 Identities = 139/199 (69%), Positives = 153/199 (76%), Gaps = 3/199 (1%) Query: 6 MKQSLR--ASLVAALLGCAALSAPRIAAADGDDTALTNLVALASQRLALAEPVAHWKWIN 63 M +S R AS + ALL A AP A ADGDDTALTNL+ALASQRLALAEPVA WKW N Sbjct: 1 MNRSYRFGASCMLALLAALAF-APAPAIADGDDTALTNLIALASQRLALAEPVARWKWAN 59 Query: 64 RKPISDPPREAALLTDVEKRATANGVDPAYARTFFDDQIAASKQLQNALFATWRATHGPE 123 + I+D PRE ALL DVEKRA A VDPA+AR FF DQI ASK +QNALFA WR + P+ Sbjct: 60 HQDITDTPRENALLADVEKRAAAANVDPAFARAFFQDQIDASKDVQNALFAAWRRSQPPQ 119 Query: 124 GPAPDLATSTRPQLDRLTQSLIAALARVAPLRDAPDCPSRLARSIANWKTLTRYDSAQKD 183 GPAPDLATSTRPQLDRLTQSL+A LARV PLR APDCPSR+A+S+ANWK+LTRYDSA Sbjct: 120 GPAPDLATSTRPQLDRLTQSLVAGLARVQPLRAAPDCPSRVAQSLANWKSLTRYDSAHSS 179 Query: 184 ALGTALSHVCAAGGASAVG 202 AL AL HVC GG A G Sbjct: 180 ALTRALGHVCETGGVGATG 198 Lambda K H 0.318 0.128 0.380 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: 203 Number of extensions: 5 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: 202 Length of database: 198 Length adjustment: 21 Effective length of query: 181 Effective length of database: 177 Effective search space: 32037 Effective search space used: 32037 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 (21.8 bits) S2: 45 (21.9 bits)
Align candidate BPHYT_RS15260 BPHYT_RS15260 (chorismate mutase)
to HMM TIGR01806 (putative chorismate mutase (EC 5.4.99.5))
# 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.aa/TIGR01806.hmm # target sequence database: /tmp/gapView.6559.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01806 [M=114] Accession: TIGR01806 Description: CM_mono2: putative chorismate mutase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-33 101.9 0.5 1.8e-33 101.3 0.5 1.2 1 lcl|FitnessBrowser__BFirm:BPHYT_RS15260 BPHYT_RS15260 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS15260 BPHYT_RS15260 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 101.3 0.5 1.8e-33 1.8e-33 4 112 .. 33 142 .. 31 144 .. 0.97 Alignments for each domain: == domain 1 score: 101.3 bits; conditional E-value: 1.8e-33 TIGR01806 4 aaldqlvdlaneRleladaValyKaesnlpieDsereeqvLdslraqaksagldedsverlfqaqinAnk 73 +al +l+ la++Rl+la++Va +K+ +++ i+D++re+++L+++ + a +a +d+ ++ +fq+qi+A+k lcl|FitnessBrowser__BFirm:BPHYT_RS15260 33 TALTNLIALASQRLALAEPVARWKWANHQDITDTPRENALLADVEKRAAAANVDPAFARAFFQDQIDASK 102 57999***************************************************************** PP TIGR01806 74 aiqyrllsdWkskaeppvevrdLe.dlRakidqlntelLe 112 +q++l++ W++++ p +++dL +R+++d l++ l+ lcl|FitnessBrowser__BFirm:BPHYT_RS15260 103 DVQNALFAAWRRSQPPQGPAPDLAtSTRPQLDRLTQSLVA 142 ***********************99**********99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (114 nodes) Target sequences: 1 (198 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: 8.59 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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