Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_086508434.1 BZY95_RS02535 aspartate aminotransferase family protein
Query= BRENDA::Q88RB9 (425 letters) >NCBI__GCF_002151265.1:WP_086508434.1 Length = 450 Score = 195 bits (495), Expect = 3e-54 Identities = 146/405 (36%), Positives = 205/405 (50%), Gaps = 26/405 (6%) Query: 28 VDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAYEPY 87 V AK + D GR+ +D G N GH + A+ QL +V+ T P Sbjct: 17 VSHAKGVYLWDETGRQYLDGCSGAISCNLGHGRNDIREAMLAQLDRVAFTYRTQFENAPA 76 Query: 88 VELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIAR---AATG---RAGVIAFTGGYHG 141 V L + + +K V++GSEAVE+A+K+AR A G R ++ YHG Sbjct: 77 VALAKALVGFTQQQLEK-VFFVSSGSEAVESALKLARQYFVARGEPQRRRFVSLRPSYHG 135 Query: 142 RTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDA-----IASVERIFKNDA 196 T+ LG+TG P A + G + P DD + + R A Sbjct: 136 STLGALGVTG-YQPLEAPFRDIAIGSLKVAGPDFYRHDDTDDGRHVARVLADTRAAIEAA 194 Query: 197 EPRDIAAIILEPVQGEG-GFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAM 255 P IAA +LEPV G G + + +RALCD+ G LLI DEV TG GRTGT+FA Sbjct: 195 GPDTIAAFVLEPVGGASTGARKLDRSYLAGIRALCDEFGCLLILDEVLTGIGRTGTWFAY 254 Query: 256 EQMGVAPDLTTFAKSI-AGGFPLAGVCGKAEYMDAI-APGGL--GGTYAGSPIACAAALA 311 + GV PDL + AK + AG +P+ V +A+ ++ + A GG G TYAG+P+ACA LA Sbjct: 255 QHYGVTPDLLSTAKGLGAGYYPVGAVLSRADIVETVMASGGFQHGHTYAGNPLACATGLA 314 Query: 312 VIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVE-VFEKGTHTPNA 370 V+E E EK+LD A G +L AGL ++ ++P +GDVRGLG + VE V + + P Sbjct: 315 VVEAIEREKILDNVAARGRQLAAGLEALKARFPWVGDVRGLGLLWGVELVADAASKAPFP 374 Query: 371 A---AVGQVVAKAREKGLILLS----CGTYGNVLRILVPLTAEDA 408 A ++ A ARE+GL++ G G+ I PLT + A Sbjct: 375 AEQNRFARITALAREEGLLIYPRRTLDGIAGDHFLITPPLTIDAA 419 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: 471 Number of extensions: 19 Number of successful extensions: 6 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: 450 Length adjustment: 32 Effective length of query: 393 Effective length of database: 418 Effective search space: 164274 Effective search space used: 164274 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