Align Anthranilate synthase component I (characterized, see rationale)
to candidate Echvi_2504 Echvi_2504 Anthranilate/para-aminobenzoate synthases component I
Query= uniprot:A0A1X9ZB07_9SPHI (466 letters) >FitnessBrowser__Cola:Echvi_2504 Length = 469 Score = 529 bits (1363), Expect = e-155 Identities = 259/467 (55%), Positives = 348/467 (74%), Gaps = 7/467 (1%) Query: 3 YKINTTYKKMLADTTTPVSIYLRLRDVYPNSILLESSDYHSRENSMSFVCADPVAGIILK 62 +KINT YKK+LADT TPVSIYL++RD + N ILLESSDYH ++NS S++C +P+A Sbjct: 7 FKINTRYKKLLADTITPVSIYLQVRDKFKNPILLESSDYHGQDNSYSYICFNPMATFSFD 66 Query: 63 GSRLETYFPDGA---VEITESKNLIEEITDFKDKFSETELPEIKFISSGLFGYFTWNAVQ 119 G + FP+ ++ E + L++++ F +F E E + KFI++GLFGY ++ V Sbjct: 67 GKTISETFPEEEKHQFDLKEGEKLVDKLKAFSSRFEE-EANDFKFITNGLFGYMQYDTVG 125 Query: 120 HFEDIKFTSETPEGEEIPEMQYHLYRYIIAIDHFKNEITLFKNTFEGEEEGGLEKMEYLI 179 FEDI T E + +P+ Y +Y+ +I +DHFKNE+ +F GE++ + ++E L+ Sbjct: 126 SFEDI--TLENTKESNVPQAFYAVYKNVIVVDHFKNELHIFDYHVNGEDDR-VREIETLL 182 Query: 180 QNKNYPEYKFQLRGEESSNLTDQGFMDLVEKLQKHIYRGDVFQIVPSRAFKQAFSGDEFN 239 N+N P Y F+L GEE+SN TD F+D++ + ++H ++GDVFQIV SR F F GDEFN Sbjct: 183 NNRNIPTYSFKLDGEETSNYTDNQFLDILRQGREHCFKGDVFQIVLSRCFTTGFKGDEFN 242 Query: 240 VYRCLRSINPSPYLFYFDYGNFKLFGSSPEAQITIKNNSANIFPIAGTFKRSGNDIEDAE 299 VYR LRS+NPSPYLFYFDYG++K+FGSSPEAQI +K A I+PIAGTFKR+GND+ DAE Sbjct: 243 VYRALRSVNPSPYLFYFDYGSYKVFGSSPEAQIVVKGRKATIYPIAGTFKRTGNDLADAE 302 Query: 300 QARKLEQDPKESAEHVMLVDLARNDLSRHCNRVEVKSFKEVQYYSHLIHLVSKVSGHLQE 359 A KL DPKE++EHVMLVDLARNDLSR +VEV+ FKE+QYYSH+IHLVSKV+G L E Sbjct: 303 LATKLYDDPKENSEHVMLVDLARNDLSRSSEKVEVEVFKEIQYYSHVIHLVSKVTGVLPE 362 Query: 360 NVSAFKVVADTYPAGTLSGAPKYKAMQLIDENEKLGRNFYAGAIGFMGFNEDFNHAIMIR 419 + ++VADT+PAGTLSGAPKY+AM++ID+ E R FY GAIGF+GFN DFNHAI+IR Sbjct: 363 TANPLQLVADTFPAGTLSGAPKYRAMEIIDKLENTSRKFYGGAIGFLGFNGDFNHAILIR 422 Query: 420 TFMSKNNELHYRAGAGIVADSVPETEMQEVNNKIAALRKAVQMAEGI 466 +F+S+NN L ++AGAG+VA S E+E+QEV NK+ ALR A++ AE + Sbjct: 423 SFVSENNRLRFQAGAGVVAKSSIESELQEVTNKLQALRVALKAAEQV 469 Lambda K H 0.318 0.135 0.386 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: 770 Number of extensions: 41 Number of successful extensions: 4 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: 466 Length of database: 469 Length adjustment: 33 Effective length of query: 433 Effective length of database: 436 Effective search space: 188788 Effective search space used: 188788 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 (21.7 bits) S2: 51 (24.3 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