Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate 353460 BT3934 putative phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase (NCBI ptt file)
Query= reanno::Pedo557:CA265_RS11635 (379 letters) >FitnessBrowser__Btheta:353460 Length = 353 Score = 377 bits (968), Expect = e-109 Identities = 181/342 (52%), Positives = 248/342 (72%), Gaps = 5/342 (1%) Query: 20 PLIISGPCSAETEEQLLTTAHLLAATGKVSVLRAGIWKPRTRPGEFEGIGSIGLEWLKRA 79 P++I+GPCSAETEEQ++ TA LAA G+ + RAGIWKPRT+PG FEGIG GL WLK Sbjct: 16 PIVIAGPCSAETEEQVMETAKQLAAKGQ-KIYRAGIWKPRTKPGGFEGIGVEGLAWLKEV 74 Query: 80 KAETGLPTAVEVANAKHVEEALAAGVDILWIGARSTVNPFTVQEIADALKGHDVPVLIKN 139 K ETG+ + EVA AKHV E L AG+DILW+GAR+T NPF VQEIADALKG D+PVL+KN Sbjct: 75 KKETGMYVSTEVATAKHVYECLKAGIDILWVGARTTANPFAVQEIADALKGVDIPVLVKN 134 Query: 140 PVNPDLQLWIGAIERINGAGITKIGAIHRGFSSFEKSSFRNEPMWELAIQLKTLCPELPI 199 PVNPDL+LWIGA+ERI+ AG+ ++GAIHRGFSS++K +RN P W + I+L+ P LPI Sbjct: 135 PVNPDLELWIGALERIHNAGLKRLGAIHRGFSSYDKKIYRNLPQWHIPIELRRRLPNLPI 194 Query: 200 INDPSHICGNRELIPYISQKALDLDMQGLMIESHVDPSVAWTDAKQQVTPAALAELVDRL 259 DPSHI G REL+ + Q+A+DL+ GL++ESH +P AW+DA QQVTP L +++ L Sbjct: 195 FCDPSHIGGKRELVAPLCQQAMDLNFDGLIVESHCNPDCAWSDASQQVTPDVLDYILNLL 254 Query: 260 TVREPEAPNEAFADKLADLRKSIDKIDDVLLQKLGERMAIVEKIGEFKRDNQVTILQVNR 319 +R E+ L+ LRK ID+ DD ++Q+L +RM + +IG +K+++ +T+LQ R Sbjct: 255 VIRTETQTTES----LSQLRKQIDECDDNIIQELAKRMRVAREIGTYKKEHGITVLQAGR 310 Query: 320 WDAIIKKGHAFAKALKLDLNFTEKFLELVHGESIRKQTEIMN 361 ++ I++K A + + +F + E +H ES+R+Q EI+N Sbjct: 311 YNEILEKRGAQGEQCGMSADFMKLIFEAIHEESVRQQIEIIN 352 Lambda K H 0.317 0.134 0.389 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: 363 Number of extensions: 10 Number of successful extensions: 3 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: 379 Length of database: 353 Length adjustment: 30 Effective length of query: 349 Effective length of database: 323 Effective search space: 112727 Effective search space used: 112727 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate 353460 BT3934 (putative phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase (NCBI ptt file))
to HMM PF01817 (CM_2)
# 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/PF01817.25.hmm # target sequence database: /tmp/gapView.10789.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CM_2 [M=79] Accession: PF01817.25 Description: Chorismate mutase type II 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-27 82.1 3.2 2.4e-27 81.5 1.5 2.2 2 lcl|FitnessBrowser__Btheta:353460 BT3934 putative phospho-2-dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:353460 BT3934 putative phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase (NCB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.2 0.0 0.16 0.16 40 53 .. 26 39 .. 23 51 .. 0.70 2 ! 81.5 1.5 2.4e-27 2.4e-27 1 78 [. 270 347 .. 270 348 .. 0.99 Alignments for each domain: == domain 1 score: -1.2 bits; conditional E-value: 0.16 CM_2 40 eReeevlerlrega 53 e ee+v+e +++ a lcl|FitnessBrowser__Btheta:353460 26 ETEEQVMETAKQLA 39 67999999999944 PP == domain 2 score: 81.5 bits; conditional E-value: 2.4e-27 CM_2 1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlregaeelgldpeavekifreiisesra 76 Rk+Ide+D+++++ la+Rm++a+ei+ yKke+g++vl+ R +e+le++ ++ e++g+++++++ if++i++es++ lcl|FitnessBrowser__Btheta:353460 270 RKQIDECDDNIIQELAKRMRVAREIGTYKKEHGITVLQAGRYNEILEKRGAQGEQCGMSADFMKLIFEAIHEESVR 345 9***************************************************9*********************** PP CM_2 77 lQ 78 +Q lcl|FitnessBrowser__Btheta:353460 346 QQ 347 99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (79 nodes) Target sequences: 1 (353 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: 8.15 // [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