Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate BWI76_RS26000 BWI76_RS26000 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Koxy:BWI76_RS26000 Length = 406 Score = 231 bits (589), Expect = 3e-65 Identities = 143/402 (35%), Positives = 213/402 (52%), Gaps = 34/402 (8%) Query: 30 RAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIE 89 + + S VWD +G+EY+DFAGGIAV GH HP ++AA+ EQ KL HT V EP + Sbjct: 30 KGKGSRVWDQQGKEYVDFAGGIAVTALGHCHPALVAALHEQGEKLWHTS-NVFTNEPALR 88 Query: 90 LAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATG------RAGVIAFTGAYHGRT 143 L ++ V F + + + SG+EA E A K+AR T + +IAF A+HGR+ Sbjct: 89 LGRKL---VDATFADRVVFMNSGTEANETAFKLARHYTVTRHSPYKTKIIAFHNAFHGRS 145 Query: 144 MMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAA 203 + T+ + G+ YS G G P I +LH V A Sbjct: 146 LFTVSVGGQP-KYSDGFGPKPADIVHVPFN-DLHAVKA--------------VMDDHTCA 189 Query: 204 IIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPD 263 +++EP+QGEGG + F+Q LR LCDQH LL+ DEVQ G GRTG+ FA G+ PD Sbjct: 190 VVVEPIQGEGGVTAATPEFLQGLRDLCDQHQALLVFDEVQCGMGRTGSLFAYMHYGVTPD 249 Query: 264 LTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLE 323 + T AK++GGGFPIS + +I A G G TY G+P+ACA A + ++L+ Sbjct: 250 ILTSAKALGGGFPISAMLTTHDIASAFHAGSHGSTYGGNPLACAVGGAAFDLINTPEVLD 309 Query: 324 RSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRARE 383 A E L++I A+ + D+RG+G ++ EL H A + + A E Sbjct: 310 GVTAKRELFVQHLQQIDARFDLFSDIRGMGLLIGAEL--KPQYHGKARD----FLYAAAE 363 Query: 384 KGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDEL 425 G+++L+ G +V+RF+ + I D+ + +G+A A+ + + Sbjct: 364 AGVMVLNAGP--DVMRFVPSLVIDDSDIAEGMARFAQAVERV 403 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: 437 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: 406 Length adjustment: 31 Effective length of query: 395 Effective length of database: 375 Effective search space: 148125 Effective search space used: 148125 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: 50 (23.9 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