Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate GFF324 PS417_01650 chorismate mutase
Query= BRENDA::B2JYH9 (182 letters) >FitnessBrowser__WCS417:GFF324 Length = 178 Score = 126 bits (316), Expect = 2e-34 Identities = 77/179 (43%), Positives = 100/179 (55%), Gaps = 7/179 (3%) Query: 3 LALALWFAAGCSPGIGAQQDAFVPLVRSMADRLNTADQVALSKWDTGQPVYDGQREAQVI 62 L AL F S A PL+ S+A+RL ADQVALSKWD+ +PV D +RE +VI Sbjct: 5 LVFALLFV---STSASAAPPTLEPLLNSIAERLEIADQVALSKWDSKKPVEDKKREQEVI 61 Query: 63 ANAATMASEYGLTAEDAINIFSDQVEANKEVQYALLNNWRRQGDAPATPRQSLAGVIRPI 122 A+ + A Y L A A FS Q+EANK VQY L++W+ QG AP PR L IRP Sbjct: 62 ASVSAQAPTYKLDAAAAEQFFSAQIEANKLVQYTHLSDWQFQGKAPDDPRPDLIKQIRPQ 121 Query: 123 LDKLQASIMQNLQSVAPLRSIADCHALVASAVGQVAEQASLDVLHRAALDRAVARICVK 181 LD+LQ ++Q L P R+ C +A AV + D L + A+ RA A +CV+ Sbjct: 122 LDELQKRLLQQLADFTPQRTDPQCPQWLAEAVHEPLN----DPLRQLAMIRATAELCVR 176 Lambda K H 0.318 0.129 0.369 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: 80 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: 182 Length of database: 178 Length adjustment: 19 Effective length of query: 163 Effective length of database: 159 Effective search space: 25917 Effective search space used: 25917 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: 44 (21.6 bits)
Align candidate GFF324 PS417_01650 (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.7947.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-39 118.8 1.7 9.4e-39 118.3 1.7 1.2 1 lcl|FitnessBrowser__WCS417:GFF324 PS417_01650 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF324 PS417_01650 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 118.3 1.7 9.4e-39 9.4e-39 5 114 .] 22 133 .. 18 133 .. 0.96 Alignments for each domain: == domain 1 score: 118.3 bits; conditional E-value: 9.4e-39 TIGR01806 5 aldqlvdlaneRleladaValyKaesnlpieDsereeqvLdslraqaksagldedsverlfqaqinAnkaiqyrll 80 l+ l++ ++eRle+ad+Val+K++s++p+eD++re++v++s++aqa+ ld+ +e++f aqi+Ank++qy l lcl|FitnessBrowser__WCS417:GFF324 22 TLEPLLNSIAERLEIADQVALSKWDSKKPVEDKKREQEVIASVSAQAPTYKLDAAAAEQFFSAQIEANKLVQYTHL 97 6788999********************************************************************* PP TIGR01806 81 sdWk.skaeppvevrdLe.dlRakidqlntelLeal 114 sdW+ + ++p +++dL ++R+++d+l+++lL++l lcl|FitnessBrowser__WCS417:GFF324 98 SDWQfQGKAPDDPRPDLIkQIRPQLDELQKRLLQQL 133 ****9999*********98***************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (114 nodes) Target sequences: 1 (178 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.05 // [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