Align 3-hydroxykynurenine transaminase; AgHKT; Alanine--glyoxylate aminotransferase; EC 2.6.1.63; EC 2.6.1.44 (characterized)
to candidate CCNA_02687 CCNA_02687 serine-pyruvate aminotransferase
Query= SwissProt::Q7PRG3 (396 letters) >FitnessBrowser__Caulo:CCNA_02687 Length = 426 Score = 224 bits (571), Expect = 4e-63 Identities = 131/366 (35%), Positives = 192/366 (52%), Gaps = 20/366 (5%) Query: 12 NPLIIPEKIMMGPGPSNCSKRVLTAMTNTVLSNFHAELFRTMDEVKDGLRYIFQTENRAT 71 N L P +++MGPGP N RVL AM+ +L F E M+EV R +FQT+NR T Sbjct: 25 NELDHPARLLMGPGPINVHPRVLRAMSVQLLGQFDPEFTGYMNEVMALYRGVFQTQNRWT 84 Query: 72 MCVSGSAHAGMEAMLSNLLEEGDRVLIAVNGIWAERAVEMSERYGADVRTIEGPPDRPFS 131 + G++ AG+EA L + L+ GD V++ G + E++ER A V +E Sbjct: 85 FTIDGTSRAGIEAALVSTLQPGDDVVVVNAGRFGLLLAEIAERCDAKVTFVEASWGAVVD 144 Query: 132 LETLARAIELHQPKCLFLTHGDSSSGLLQPLEGVGQICHQHDCLLIVDAVASLCGVPFYM 191 + + A++ +P+ + HGD+S+ + QPL +G IC H L+ VDA A+L G+ + Sbjct: 145 PQAVEDAVKRVKPRLVACVHGDTSTTMAQPLGEIGAICRAHGALMYVDATATLSGMDVPV 204 Query: 192 DKWEIDAVYTGAQKVLGAPPGITPISISPKALDVIRNRRTKSKVF--------------- 236 D W D V G QK LG P G PI+IS +A + I +RR K Sbjct: 205 DAWGADIVTAGLQKCLGGPSGSAPITISDQAAEHIFSRRHVEKGLAGTGGAAGAGRRIAS 264 Query: 237 -YWDLLLLGNYWGCYDEPKRYHHTVASNLIFALREALAQIAEEGLENQIKRRIECAQILY 295 Y+DL ++ +YW E + HHT + ++FA RE + EEGL + R + + Sbjct: 265 NYFDLAMIMDYW---SEKRLNHHTECAPMLFAARECARLVLEEGLPARFDRHAQAGAAMT 321 Query: 296 EGLGKMGLDIFVKDPRHRLPTVTGIMIPKGVDWWKVSQYAMNNFSLEVQGGLGPTFGKAW 355 GL MGL I+ D H++ VTGI +PKGVD+ +V +F +E+ GP GK W Sbjct: 322 AGLEAMGLSIY-GDKAHKMTNVTGIWVPKGVDYDRVKARMRTDFEIEIGSAFGPLTGKIW 380 Query: 356 RVGIMG 361 R+G MG Sbjct: 381 RIGTMG 386 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: 428 Number of extensions: 16 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: 396 Length of database: 426 Length adjustment: 31 Effective length of query: 365 Effective length of database: 395 Effective search space: 144175 Effective search space used: 144175 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