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)
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