Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_076582365.1 BB347_RS07365 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_001971705.1:WP_076582365.1 Length = 439 Score = 246 bits (629), Expect = 8e-70 Identities = 147/410 (35%), Positives = 220/410 (53%), Gaps = 16/410 (3%) Query: 26 VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYE 85 V +RA T+ D +G EY+D GI+V N GH + V+ A ++QL + H C V Sbjct: 29 VPIKRASGETLEDFDGNEYLDAFSGISVTNVGHNNEAVVEAAKDQLDEFVHGCSYVHPNA 88 Query: 86 PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMM 145 P ELAE +A PGD K + SG+EAVE A+K+AR TG V+A +HGRT+ Sbjct: 89 PVGELAERLASETPGDLTK-SFFCNSGTEAVEGAIKLARKYTGSTEVLALEMGFHGRTLG 147 Query: 146 TLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIAS------IERIFKNDAQPQ 199 +L LTG Y GM + P S + + +ER+ Sbjct: 148 SLALTGNKA-YKNGMAPTINDVSHVEPPYGYRCPSCEGETCTAACAENVERVIGTHTA-D 205 Query: 200 DIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLG 259 D+AAI++EPV GEGG V + +++R++ + +H LLIADEVQTG GRTG +A + Sbjct: 206 DLAAIVVEPVMGEGGIIVPPEGWLERVQEIAHEHDALLIADEVQTGYGRTGELWAVDHFD 265 Query: 260 IVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEE 319 +VPD+ T AK + G P+ + EI DA G T+ G+P+ACAAALA L+ ++ Sbjct: 266 VVPDIITQAKGIANGLPLGAFTAREEIADAFESGDHLSTFGGNPVACAAALATLEEL-QD 324 Query: 320 KLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFE------GGDTHKPAAEL 373 +++ ++ G L+ L ++++ V+GD RGLG M +E+ + G P A+L Sbjct: 325 GIIDNAREQGAWLEDELAALESEFDVVGDTRGLGLMYGLEIVDPSTDGPRGVAPAPDAKL 384 Query: 374 VSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFD 423 + RE+G+++ G Y NVIR P+TI +QLE+ +A L + Sbjct: 385 AKSVAADLREEGIVIGVGGYYSNVIRLQPPLTIDRSQLERIVAALRSALE 434 Lambda K H 0.319 0.137 0.393 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: 466 Number of extensions: 23 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: 426 Length of database: 439 Length adjustment: 32 Effective length of query: 394 Effective length of database: 407 Effective search space: 160358 Effective search space used: 160358 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 Sep 24 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