Align Transaminase BacF; Transaminase A; EC 2.6.1.- (characterized)
to candidate WP_066328699.1 BLR17_RS00150 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P39643 (399 letters) >NCBI__GCF_900100165.1:WP_066328699.1 Length = 381 Score = 276 bits (706), Expect = 7e-79 Identities = 146/381 (38%), Positives = 221/381 (58%), Gaps = 2/381 (0%) Query: 3 ITPSDVIKTLPRQEFSLVFQKVKEMEKTGAHIINLGQGNPDLPTPPHIVEALREASLNPS 62 IT ++ + T+ FS ++V+++ G IIN+G G+PDL +++A+ A + + Sbjct: 2 ITTANRLNTVEEYYFSSKLREVRQLAAEGKPIINMGIGSPDLAPAQAVIDAVALAMQDVN 61 Query: 63 FHGYGPFRGYPFLKEAIAAFYKREYGVTINPETEVALFGGGKAGLYVLTQCLLNPGDIAL 122 HGY ++G P L++++A FY+ + V +NP TE+ G K G+ ++ LN GD L Sbjct: 62 AHGYQSYQGLPELRKSMADFYQNNFQVALNPNTEILPLMGSKEGIMHISMAFLNEGDQVL 121 Query: 123 VPNPGYPEYLSGITMARAELYEMPLYEENGYLPDFEKIDPAVLEKAKLMFLNYPNNPTGA 182 +PNPGYP Y S + AE L E N + PDFE ++ L K KLM++ YP+ PTGA Sbjct: 122 IPNPGYPTYTSVTNLVGAEAVYYDLAEANNWEPDFEALEKLDLSKVKLMWIGYPHMPTGA 181 Query: 183 VADAAFYAKAAAFAKEHNIHLIHDFAYGAFEFDQKPASFLEAEDAKTVGAELYSFSKTFN 242 A + K AFAK+H I L++D Y +F + P S L+ E AK V EL S SKTFN Sbjct: 182 RGSLALFEKLVAFAKKHQILLVNDNPY-SFVLNDNPMSLLQVEGAKEVALELNSLSKTFN 240 Query: 243 MAGWRMAFAVGNEKIIQAVNEFQDHVFVGMFGGLQQAASAALSGDPEHTESLKRIYKERI 302 MAGWR+ GN ++I AV + ++ GMF G+Q+ A AL D S+ IYK+R Sbjct: 241 MAGWRVGMVSGNAELIDAVLRVKSNMDSGMFFGIQKGAIEALKSDKSWFNSMNEIYKKRR 300 Query: 303 DFFTALCEKELGWKMEKPKGTFYVWAEIPNTFETSHQFSDYLLEHAHVVVTPGEIFGSNG 362 L EK LG K+ K +VWA++P E++ +F D +L ++ + PG IFGSNG Sbjct: 301 VLTEQLAEK-LGCKVYKEGVGLFVWAKLPEGIESAEKFIDQILHEKYIFIAPGTIFGSNG 359 Query: 363 KRHVRISMVSKQEDLREFVTR 383 + ++R ++ K+E ++E + R Sbjct: 360 EGYIRFALCVKEEKVQEAIDR 380 Lambda K H 0.319 0.137 0.407 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: 389 Number of extensions: 17 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: 399 Length of database: 381 Length adjustment: 30 Effective length of query: 369 Effective length of database: 351 Effective search space: 129519 Effective search space used: 129519 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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