Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate BWI76_RS14020 BWI76_RS14020 aspartate aminotransferase family protein
Query= BRENDA::Q88RB9 (425 letters) >FitnessBrowser__Koxy:BWI76_RS14020 Length = 461 Score = 237 bits (604), Expect = 6e-67 Identities = 152/404 (37%), Positives = 222/404 (54%), Gaps = 19/404 (4%) Query: 25 PIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAY 84 P+ + A+ + D + ++ +D G L GH HP V+ ++Q +T L Sbjct: 42 PLAITKAEGVWLTDADNKQYLDCLAGAGTLALGHNHPDVLQSIQSVITSGLPLHTLDLTT 101 Query: 85 EPYVELCEKINKLVPGDFDKKTLLVT--TGSEAVENAVKIARAATGRAGVIAFTGGYHGR 142 E + L+PG+ + L T +G++AVE A+K+A+ TGR+ VI+F+GGYHG Sbjct: 102 PLKDRFSEYLLSLLPGEGKEYCLQFTGPSGADAVEAALKLAKKYTGRSSVISFSGGYHGM 161 Query: 143 TMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELH---GISVDDAIASVERIFKN----- 194 T L +TG + P +A G+MP F +P + GI + + ++ F+N Sbjct: 162 THGALSVTGNLSPKAAVNGMMPEVQFMP-YPHQYRCPLGIGGEAGVKALTYYFENLINDV 220 Query: 195 DAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFA 254 ++ R AA+ILE VQGEGG PAP E ++R+R + +HGILLI DEVQ G RTG FFA Sbjct: 221 ESGVRKPAAVILEAVQGEGGVNPAPVEWLQRIRKVTQEHGILLIIDEVQAGFARTGKFFA 280 Query: 255 MEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVIE 314 E G+ PD+ +K++ GG PLA V G + DA PG GT+ G+ +A A L + Sbjct: 281 FEHAGIEPDIIVMSKAVGGGLPLA-VLGIKKQFDAWEPGHHTGTFRGNQLAMATGLTTLR 339 Query: 315 VFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEVF---EKGTHTPNAA 371 ++ K+ D++ A GE L L E+QK+YP+IG VRGLG MI +E+ E H Sbjct: 340 HLKDNKIADKTAAQGEWLKGKLAEMQKRYPVIGHVRGLGLMIGIEIVKPNEAPDHMGCYP 399 Query: 372 AVGQVVA----KAREKGLILLSCGTYGNVLRILVPLTAEDALLD 411 A G++ A K E GLIL G +G VLR+L L +A L+ Sbjct: 400 ADGELSALLQKKCFEAGLILERGGRHGCVLRLLPSLLISNAELE 443 Lambda K H 0.320 0.138 0.395 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: 545 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: 425 Length of database: 461 Length adjustment: 32 Effective length of query: 393 Effective length of database: 429 Effective search space: 168597 Effective search space used: 168597 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 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