Align Anthranilate synthase; EC 4.1.3.27 (characterized, see rationale)
to candidate 6935915 Sama_0130 menaquinone-specific isochorismate synthase, putative (RefSeq)
Query= uniprot:B8DM47_DESVM (520 letters) >FitnessBrowser__SB2B:6935915 Length = 452 Score = 108 bits (270), Expect = 4e-28 Identities = 79/245 (32%), Positives = 119/245 (48%), Gaps = 13/245 (5%) Query: 267 QVVLSTRFQASFSG--DPFTLYRRLRRINPSPYMF-FMRLPGVSLLGSSPEVMVRCRADK 323 +VVLS Q + DP+ + + PS + F F + + SPE + R + Sbjct: 209 KVVLSRLSQLEINDPVDPWMVLACWQGRCPSSFQFGFQFSKDRTFISCSPERLYLRRGQE 268 Query: 324 LQVSPIAGTRPRGTDDAHDAALARELLEDPKERAEHVMLVDLGRNDLGRIAAPGT--VQV 381 L +AGT RG + DA LA++L ED K E+ ++ R + +P + V Sbjct: 269 LFTEALAGTTLRGHTEEEDALLAKQLQEDSKNSHENQLV----RQHIVEHLSPLSHYVGA 324 Query: 382 ERFMDVEKFSHVMHLTSRVTAQIEPGRDALDVLAATFPAGTVSGAPKVRAMEIISEAEGL 441 E + K H+ HL + A+++PG + +L A P V G P+ A+ I + EG Sbjct: 325 EESPRIFKLPHIQHLHRAIRAELKPGINDFQLLLALHPTPAVGGLPRPSALSFIRQQEGY 384 Query: 442 ARGPYAGAIGWLGLDRDSVNLDTGITIRSLWVRDGQVHWQAGAGIVFDSVPEMEWKECNN 501 RG YAGA G+L + + IRS + G+++ AGAGIV S PE EW+E +N Sbjct: 385 NRGWYAGACGYLNRHES----EFSVAIRSALIEPGRINLFAGAGIVAGSDPEAEWQELDN 440 Query: 502 KAAVI 506 K A I Sbjct: 441 KLATI 445 Lambda K H 0.320 0.137 0.413 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: 511 Number of extensions: 20 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: 520 Length of database: 452 Length adjustment: 34 Effective length of query: 486 Effective length of database: 418 Effective search space: 203148 Effective search space used: 203148 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: 52 (24.6 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