Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate Pf6N2E2_3822 Periplasmic chorismate mutase I precursor (EC 5.4.99.5)
Query= BRENDA::B2JYH9 (182 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3822 Length = 187 Score = 125 bits (313), Expect = 6e-34 Identities = 73/181 (40%), Positives = 100/181 (55%), Gaps = 5/181 (2%) Query: 1 MTLALALWFAAGCSPGIGAQQ-DAFVPLVRSMADRLNTADQVALSKWDTGQPVYDGQREA 59 + LAL+ A + A+ +A PL+ ++ +RL DQVALSKWD+ +PV D QRE Sbjct: 7 LCLALSAALLASTAEAASARAPEALTPLLNAIGERLALGDQVALSKWDSHKPVEDRQRER 66 Query: 60 QVIANAATMASEYGLTAEDAINIFSDQVEANKEVQYALLNNWRRQGDAPATPRQSLAGVI 119 +VIA A A Y L+ E F+ Q+EANK VQY L++W +G AP PR L G I Sbjct: 67 EVIAAAVAQAPAYKLSGETVEAFFAAQIEANKMVQYINLSDWALEGKAPDLPRPDLVGEI 126 Query: 120 RPILDKLQASIMQNLQSVAPLRSIADCHALVASAVGQVAEQASLDVLHRAALDRAVARIC 179 RP LD+LQ ++Q L AP R+ C +A A + +HR AL RA +C Sbjct: 127 RPQLDRLQKRLLQQLADFAPYRTDPQCPQWLARATHHNKQHP----VHRLALIRATGELC 182 Query: 180 V 180 + Sbjct: 183 I 183 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: 98 Number of extensions: 4 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: 182 Length of database: 187 Length adjustment: 19 Effective length of query: 163 Effective length of database: 168 Effective search space: 27384 Effective search space used: 27384 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 Pf6N2E2_3822 (Periplasmic chorismate mutase I precursor (EC 5.4.99.5))
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.29895.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-38 115.6 0.1 8.8e-38 115.2 0.1 1.2 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3822 Periplasmic chorismate mutase I Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3822 Periplasmic chorismate mutase I precursor (EC 5.4.99.5) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 115.2 0.1 8.8e-38 8.8e-38 4 114 .] 29 141 .. 26 141 .. 0.97 Alignments for each domain: == domain 1 score: 115.2 bits; conditional E-value: 8.8e-38 TIGR01806 4 aaldqlvdlaneRleladaValyKaesnlpieDsereeqvLdslraqaksagldedsverlfqa 67 +al l++++ eRl+l+d+Val+K++s++p+eD++re++v++ + aqa++ l+ + ve +f+a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3822 29 EALTPLLNAIGERLALGDQVALSKWDSHKPVEDRQREREVIAAAVAQAPAYKLSGETVEAFFAA 92 5788899********************************************************* PP TIGR01806 68 qinAnkaiqyrllsdWk.skaeppvevrdLe.dlRakidqlntelLeal 114 qi+Ank++qy lsdW + ++p +++dL ++R+++d l+++lL++l lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3822 93 QIEANKMVQYINLSDWAlEGKAPDLPRPDLVgEIRPQLDRLQKRLLQQL 141 *****************9*****************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (114 nodes) Target sequences: 1 (187 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: 7.80 // [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