Align 4-aminobutyrate-pyruvate transaminase (EC 2.6.1.96) (characterized)
to candidate GFF2189 PS417_11165 omega amino acid--pyruvate aminotransferase
Query= BRENDA::Q7XN12 (497 letters) >FitnessBrowser__WCS417:GFF2189 Length = 431 Score = 268 bits (685), Expect = 3e-76 Identities = 160/439 (36%), Positives = 245/439 (55%), Gaps = 14/439 (3%) Query: 49 SMLAPFTAGWHSTDLEPLIIERSEGSYVYDSKGNKYLDTLAGLWCTALGGSEPRLVKAAT 108 S+ APFTA + +P++ +R+ G + ++G LD +AGLWC G +PR+V+A Sbjct: 4 SLWAPFTA-MRPFNRQPMLFDRAAGMHYTTTEGRDVLDAMAGLWCVNAGHGQPRIVEAIR 62 Query: 109 DQLNKLPFYHSFWNSTAKPPLDLAEELISMFTAKEMGKVFFTNSGSEANDSQVKLVWYYN 168 + +L F SF + L LA++L++ A + KVFFTNSGSEA D+ +K+ Y+ Sbjct: 63 EAAGRLDFVSSF-KMSHPAALTLADQLVAKAPAN-LDKVFFTNSGSEAVDTALKIARAYH 120 Query: 169 NALGRPNKKKIIAQSQAYHGSTLISASLSGLPAMHLKFDLPAPFVLHTDCPHYW--RFGL 226 A G + K+I +++ YHG S+SG+ F V H P+ RF L Sbjct: 121 QARGDSRRTKLIGRAKGYHGMGFGGLSVSGIGRQKRDFGPLLGDVAHLPLPYDAGSRFSL 180 Query: 227 PGEAEEEFATRLADNLENLILKEGPETVAAFIAEPVIGAGGVIPPPKTYFEKIQAVLQKY 286 + E AD L +L+ P TVAA I EPV G+GGV PP Y +K++ + ++ Sbjct: 181 ---GQPEQGAHYADALLHLLEVHDPATVAAVIVEPVTGSGGVYAPPLGYLQKLREICDRH 237 Query: 287 DVLFIADEVITGFGRLGTMFGSDLYNIKPDLVSLAKALSSAYVPIGATLVSPEISDVVHS 346 +L I DEVITGFGR+G F ++ + + PDL++LAK L++ VP+G LVS + + Sbjct: 238 GLLLIFDEVITGFGRVGHGFAAEAFGVTPDLMTLAKGLTNGAVPMGGVLVSGAVYEAFMQ 297 Query: 347 QSNKIGFFAHGFTYSGHPVSCAVALEALKIYRERNIPAHVKQISPRFQEGIKAFAGSSII 406 + HG+TYS HP++CA L L+++ E + AHV+QI+P +Q A +++ Sbjct: 298 GPEQAIELMHGYTYSAHPLACAAGLATLEVHEELGLNAHVRQIAPLWQNTALALREQALV 357 Query: 407 GETRGVGLLLATEFANNKSPNDPFPVEWGVAQIFGAECKKRGMLVKVVGDEIAMSPPLIM 466 + R +GLL A E + P GVAQ C + G+LV+ G+ I +SPPLI+ Sbjct: 358 LDVRAIGLLCAVELKPREGA--PGARAAGVAQ----RCFEAGVLVRASGENIVLSPPLII 411 Query: 467 SQREVDGLVSIYGEALKAT 485 +Q +V + S G+AL+AT Sbjct: 412 NQEQVAQVFSTLGKALEAT 430 Lambda K H 0.317 0.134 0.396 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: 471 Number of extensions: 20 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: 497 Length of database: 431 Length adjustment: 33 Effective length of query: 464 Effective length of database: 398 Effective search space: 184672 Effective search space used: 184672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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