Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate HSERO_RS02155 HSERO_RS02155 chorismate mutase
Query= BRENDA::Q2SY64 (202 letters) >FitnessBrowser__HerbieS:HSERO_RS02155 Length = 189 Score = 100 bits (250), Expect = 1e-26 Identities = 61/141 (43%), Positives = 74/141 (52%), Gaps = 6/141 (4%) Query: 12 ASLVAALLGCAALSAPRIAAADGDDTALTNLVALASQRLALAEPVAHWKWINRKPISDPP 71 A + LL A S P +D + L++L RL +A PVA KW + PI DP Sbjct: 13 ALIATLLLSACATSTPPAVRSD-----VEQLLSLQKTRLDVAAPVARSKWNSHAPIDDPA 67 Query: 72 REAALLTDVEKRATANGVDPAYARTFFDDQIAASKQLQNALFATWRATHGPE-GPAPDLA 130 REA +L DV RA G+D A+ R FF DQ A K +Q L WR P PDLA Sbjct: 68 REAVILDDVAARAQKLGLDAAWTRRFFQDQFEAGKIVQRDLHRQWRVEQRPPFANPPDLA 127 Query: 131 TSTRPQLDRLTQSLIAALARV 151 RP LDRLT L+AALAR+ Sbjct: 128 LQVRPVLDRLTPDLLAALARL 148 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: 142 Number of extensions: 10 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: 202 Length of database: 189 Length adjustment: 20 Effective length of query: 182 Effective length of database: 169 Effective search space: 30758 Effective search space used: 30758 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: 44 (21.6 bits)
Align candidate HSERO_RS02155 HSERO_RS02155 (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.12613.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-33 99.0 0.4 1.2e-32 98.6 0.4 1.2 1 lcl|FitnessBrowser__HerbieS:HSERO_RS02155 HSERO_RS02155 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS02155 HSERO_RS02155 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 98.6 0.4 1.2e-32 1.2e-32 4 114 .] 33 145 .. 30 145 .. 0.97 Alignments for each domain: == domain 1 score: 98.6 bits; conditional E-value: 1.2e-32 TIGR01806 4 aaldqlvdlaneRleladaValyKaesnlpieDsereeqvLdslraqaksagldedsverlfqaqinA 71 ++++ql++l + Rl +a +Va +K++s+ pi+D++re+ +Ld+++a a+++gld+ +r+fq+q +A lcl|FitnessBrowser__HerbieS:HSERO_RS02155 33 SDVEQLLSLQKTRLDVAAPVARSKWNSHAPIDDPAREAVILDDVAARAQKLGLDAAWTRRFFQDQFEA 100 5899**************************************************************** PP TIGR01806 72 nkaiqyrllsdWk.skaeppvevrdLe.dlRakidqlntelLeal 114 k++q l +W+ +++ p +++dL ++R+ +d l+ lL al lcl|FitnessBrowser__HerbieS:HSERO_RS02155 101 GKIVQRDLHRQWRvEQRPPFANPPDLAlQVRPVLDRLTPDLLAAL 145 *************99999999********************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (114 nodes) Target sequences: 1 (189 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: 8.41 // [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