Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_086510803.1 BZY95_RS15480 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::Q88RB9 (425 letters) >NCBI__GCF_002151265.1:WP_086510803.1 Length = 430 Score = 436 bits (1122), Expect = e-127 Identities = 212/421 (50%), Positives = 287/421 (68%), Gaps = 1/421 (0%) Query: 5 NESLMQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVV 64 N L + + V G F D A+N+ + D +G +IDFAGGI VLN GH HPKVV Sbjct: 3 NAQLNELKQRYVANGAASPATQFADRAENALIWDADGNRIIDFAGGIGVLNIGHRHPKVV 62 Query: 65 AAVQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIAR 124 AV+ QL KV HTC V+ YE YV++ EK++++ P K +L +G+EA+ENAVKIAR Sbjct: 63 EAVKAQLDKVMHTCQTVMPYEGYVKVAEKLSQVTPVRGHAKVMLANSGAEALENAVKIAR 122 Query: 125 AATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDA 184 AATG+ VI F GGYHGRT MT+ + GKV PY++ G MPG +FRA +P HG+S D+A Sbjct: 123 AATGKNNVICFDGGYHGRTFMTMAMNGKVAPYASDFGTMPGNVFRAPYPVPYHGVSEDEA 182 Query: 185 IASVERIFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQT 244 I ++ K DA PRD AAI+LEPV GEGGF PAP +K +R +CD+HG+L+I DEVQ+ Sbjct: 183 IRGLKMAIKTDANPRDTAAIVLEPVLGEGGFYPAPASFLKAIREICDEHGMLMIVDEVQS 242 Query: 245 GAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPI 304 G GRTG FA+E GV PD+ T AKS+A G P++ V G + MDA P LGGTY G+P+ Sbjct: 243 GFGRTGKLFAIEHSGVEPDIITMAKSMADGMPISAVVGTDKVMDASGPNSLGGTYTGNPL 302 Query: 305 ACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVE-VFEK 363 +CAA LAV++VFEEE +L++S A+G++L + Q+ + + + R +G+M A++ V +K Sbjct: 303 SCAATLAVLDVFEEENILEKSMALGDKLAKRFAQWQRDFDCVDNARNMGAMAALDLVTDK 362 Query: 364 GTHTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECFAE 423 HTP+A + KAREKGLILLSCG YGN +R L+P+T ED +L++GL I+E E Sbjct: 363 AKHTPDADLAAALCKKAREKGLILLSCGLYGNTIRFLMPVTIEDEILEEGLDIVEAALTE 422 Query: 424 I 424 + Sbjct: 423 L 423 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: 503 Number of extensions: 10 Number of successful extensions: 2 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: 430 Length adjustment: 32 Effective length of query: 393 Effective length of database: 398 Effective search space: 156414 Effective search space used: 156414 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