Align 3-hydroxykynurenine transaminase; AgHKT; Alanine--glyoxylate aminotransferase; EC 2.6.1.63; EC 2.6.1.44 (characterized)
to candidate BWI76_RS10590 BWI76_RS10590 class V aminotransferase
Query= SwissProt::Q7PRG3 (396 letters) >FitnessBrowser__Koxy:BWI76_RS10590 Length = 413 Score = 232 bits (591), Expect = 2e-65 Identities = 130/362 (35%), Positives = 203/362 (56%), Gaps = 22/362 (6%) Query: 17 PEKIMMGPGPSNCSKRVLTAMTNTVLSNFHAELFRTMDEVKDGLRYIFQTENRATMCVSG 76 P +++MGPGP N RVL AM++ ++ + + M+EV R +F+TENR TM V G Sbjct: 12 PSRLLMGPGPINADPRVLRAMSSQLIGQYDPAMTHYMNEVMALYRGVFRTENRWTMLVDG 71 Query: 77 SAHAGMEAMLSNLLEEGDRVLIAVNGIWAERAVEMSERYGADVRTIEGPPDRPFSLETLA 136 ++ AG+EA+L + + GD+VL+ V G + E++ R A+V TIE P F+ + + Sbjct: 72 TSRAGIEAILVSAIRPGDKVLVPVFGRFGHLLCEIARRCRAEVHTIEVPWGEVFTPDQVE 131 Query: 137 RAIELHQPKCLFLTHGDSSSGLLQPLEGVGQICHQHDCLLIVDAVASLCGVPFYMDKWEI 196 A++ +P+ L GD+S+ +LQPL +G+IC ++D L DA ASL G P D W + Sbjct: 132 DAVKRIRPRLLLTVQGDTSTTMLQPLAELGEICRRYDALFYTDATASLGGNPLETDVWGL 191 Query: 197 DAVYTGAQKVLGAPPGITPISISPKALDVIRNRRTKSKVF----------------YWDL 240 DAV G QK LG P G +PI++S + + IR R+ + Y+DL Sbjct: 192 DAVSAGMQKCLGGPSGTSPITLSARMEEAIRRRKCVEEGIRTDAHRDGDEEMIYSNYFDL 251 Query: 241 LLLGNYWGCYDEPKRY-HHTVASNLIFALREALAQIAEEGLENQIKRRIECAQILYEGLG 299 ++ +YWG P+R HHT A+ +F RE I +EGL+ I R L +G+ Sbjct: 252 GMVMDYWG----PERLNHHTEATTALFGARECARLILQEGLDYGIARHKLHGDALVKGIQ 307 Query: 300 KMGLDIFVKDPRHRLPTVTGIMIPKGVDWWKVSQYAMNNFSLEVQGGLGPTFGKAWRVGI 359 MGL+ F D +H++ V G++IP+G++ + + + +F +E+ GP GK WR+G Sbjct: 308 AMGLETF-GDLKHKMNNVLGVVIPQGINGDQARKLMLEDFGIEIGTSFGPLHGKVWRIGT 366 Query: 360 MG 361 MG Sbjct: 367 MG 368 Lambda K H 0.321 0.138 0.430 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: 437 Number of extensions: 21 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: 396 Length of database: 413 Length adjustment: 31 Effective length of query: 365 Effective length of database: 382 Effective search space: 139430 Effective search space used: 139430 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 (21.9 bits) S2: 50 (23.9 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