Align Secreted chorismate mutase; CM; EC 5.4.99.5 (characterized)
to candidate WP_036377464.1 MVAN_RS25525 gamma subclass chorismate mutase AroQ
Query= SwissProt::A0QU81 (181 letters) >NCBI__GCF_000015305.1:WP_036377464.1 Length = 185 Score = 197 bits (501), Expect = 9e-56 Identities = 97/178 (54%), Positives = 128/178 (71%) Query: 4 SVALAALAGVGTPHATADDASPLVPLVDAAAQRLQTADPVAASKFRSGGAIDDPDREQQV 63 +VA+AAL + P A A + LV LVDAA +RLQ A+P+AA+KF +GG I+DP REQQV Sbjct: 8 AVAMAALLPLFAPAAAAQPQTTLVDLVDAATRRLQVAEPIAANKFHTGGLIEDPVREQQV 67 Query: 64 IAAVTGDATRHNIDPGYVHDVFRNQIDATSSVEHTRFAQWKLDPAAAPSSAPDLSESRQK 123 + AV+ +AT ++DP YV FR+QIDAT ++E++R AQWK DPA AP APDL+ SR Sbjct: 68 LDAVSAEATALDLDPAYVTTAFRDQIDATVAIEYSRLAQWKFDPATAPVDAPDLASSRGI 127 Query: 124 IDTLNRTMVDEIARQWPVLHSPVCRPDLDRALDAVATARGFDPVYRHALEYATHSYCR 181 ID LNR MV +A +W LH+P CR +LD+A VA RG DP+YR A+++AT +YCR Sbjct: 128 IDALNREMVTLMADEWDKLHAPTCRAELDQAKATVAAQRGLDPLYRQAVDHATRNYCR 185 Lambda K H 0.318 0.130 0.387 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: 162 Number of extensions: 8 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: 181 Length of database: 185 Length adjustment: 19 Effective length of query: 162 Effective length of database: 166 Effective search space: 26892 Effective search space used: 26892 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 (21.7 bits) S2: 44 (21.6 bits)
Align candidate WP_036377464.1 MVAN_RS25525 (gamma subclass chorismate mutase AroQ)
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.4566.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-32 98.2 0.1 2.9e-32 97.4 0.1 1.3 1 lcl|NCBI__GCF_000015305.1:WP_036377464.1 MVAN_RS25525 gamma subclass chor Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_036377464.1 MVAN_RS25525 gamma subclass chorismate mutase AroQ # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 97.4 0.1 2.9e-32 2.9e-32 4 112 .. 28 137 .. 25 139 .. 0.97 Alignments for each domain: == domain 1 score: 97.4 bits; conditional E-value: 2.9e-32 TIGR01806 4 aaldqlvdlaneRleladaValyKaesnlpieDsereeqvLdslraqaksagldedsverlfqaqinAn 72 + l lvd+a Rl++a+++a+ K++ + ieD+ re+qvLd ++a+a ++ ld+ +v+ f +qi+A+ lcl|NCBI__GCF_000015305.1:WP_036377464.1 28 TTLVDLVDAATRRLQVAEPIAANKFHTGGLIEDPVREQQVLDAVSAEATALDLDPAYVTTAFRDQIDAT 96 46789**************************************************************** PP TIGR01806 73 kaiqyrllsdWk.skaeppvevrdLedlRakidqlntelLe 112 ai+y++l++Wk +a++pv+++dL +R id+ln e+++ lcl|NCBI__GCF_000015305.1:WP_036377464.1 97 VAIEYSRLAQWKfDPATAPVDAPDLASSRGIIDALNREMVT 137 ***************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (114 nodes) Target sequences: 1 (185 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: 5.07 // [ok]
This GapMind analysis is from Apr 10 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