Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate RR42_RS27380 RR42_RS27380 4-aminobutyrate aminotransferase
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__Cup4G11:RR42_RS27380 Length = 435 Score = 304 bits (778), Expect = 5e-87 Identities = 170/426 (39%), Positives = 244/426 (57%), Gaps = 7/426 (1%) Query: 59 PSTAEIIAKRREFLSPALFHFYNTPLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCH 118 PS A + +R L PA FY PL+IV +++D NG RYLDA+ +A+V GHCH Sbjct: 8 PSVAALTERRARVLGPAYRLFYEEPLHIVRGDGVWLYDANGERYLDAYNNVASV--GHCH 65 Query: 119 PEVVNSVVKQLKLINHSTILYLNHTISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMM 178 P+VV ++ +Q +N T YL+ I D+A+ L++T+P L T +G+EAN+LAM + Sbjct: 66 PQVVQAIARQAAQLNTHT-RYLHEGILDYAQRLLATMPDALGHAMLTCTGSEANDLAMRI 124 Query: 179 ARLYTGCNDIVSLRNSYHGNAAATMGATAQSNWKFNVVQSGVHHAINPDPYRGIFGSDGE 238 AR +TG ++ R +YHG A++ + S ++ + V PD YR + G Sbjct: 125 ARAHTGAQGLIITRFAYHG-VTASIAEASPSLGRYVKLGDNVRTVPAPDSYRVVPAQLGA 183 Query: 239 KYASDVHDLIQFGTSGQV--AGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADE 296 +A V I+ + + A + +++ GI PG+L A +R AGGV IADE Sbjct: 184 VFAEGVRHAIEDLRAHGIRPAALLVDTVFSSDGIFTDPPGFLKDAVAAIRAAGGVFIADE 243 Query: 297 VQSGFARTGTHFWGFQSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRS-YFNTF 355 VQ G RTG FWGFQ HGV+PDIVTM K +GNG PL + PE+ R YFNTF Sbjct: 244 VQPGLGRTGEAFWGFQRHGVVPDIVTMGKPMGNGHPLAGLAVRPEVLEAFGRECRYFNTF 303 Query: 356 GGNPMCTAAGHAVLRVLHEEKLQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGVE 415 GGNP+ AAG AVL V+ + +L VG +L+ RL + + LIGD+RG GL + VE Sbjct: 304 GGNPVSVAAGMAVLDVIEQTQLMAQVRRVGKYLRERLAGVAARRPLIGDIRGAGLFVAVE 363 Query: 416 FVKDRDLKTPAKAETLHLMDQMKEMGVLVGKGGFYGNVFRITPPLCFTLSDADFLVDVMD 475 FV+D D PA A T +++ ++ VLVG G N+ +I PP+ FT + AD L D +D Sbjct: 364 FVEDGDAARPATARTARIVNGLRRRHVLVGATGEAANILKIRPPMVFTEAHADLLADTLD 423 Query: 476 HAMSKM 481 ++++ Sbjct: 424 AVLAEV 429 Lambda K H 0.320 0.136 0.406 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: 506 Number of extensions: 20 Number of successful extensions: 5 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: 481 Length of database: 435 Length adjustment: 33 Effective length of query: 448 Effective length of database: 402 Effective search space: 180096 Effective search space used: 180096 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: 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