Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_085639734.1 MGEO_RS15340 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::Q88RB9 (425 letters) >NCBI__GCF_002115805.1:WP_085639734.1 Length = 460 Score = 490 bits (1261), Expect = e-143 Identities = 250/422 (59%), Positives = 313/422 (74%), Gaps = 3/422 (0%) Query: 5 NESLMQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVV 64 N +L RR AV RGVG P+F A+N+ + DVEG+ IDFAGGIAVLNTGH HP V+ Sbjct: 28 NAALWARRETAVARGVGSAAPVFAARAENAELWDVEGKRYIDFAGGIAVLNTGHRHPSVI 87 Query: 65 AAVQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIAR 124 AA + Q +HT FQV+ YEPY+ L EK+N L PGDF KKTLLVTTG+EAVENAVKIAR Sbjct: 88 AAAKAQEDLYTHTSFQVVPYEPYIALAEKLNALAPGDFAKKTLLVTTGAEAVENAVKIAR 147 Query: 125 AATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDA 184 A TGR GVIAFT GYHGRT++TLGLTGKV PY +G P IFRA FP G++V D+ Sbjct: 148 AHTGRPGVIAFTAGYHGRTLLTLGLTGKVNPYKKDVGPFPSDIFRAPFPDTRAGLTVSDS 207 Query: 185 IASVERIFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQT 244 + ++E +F DA+P +AAIILEPV GEGG+ P P E+ + LRA+CD+HGILLI+DE+Q Sbjct: 208 LRALETLFLTDAQPDRVAAIILEPVLGEGGYHPVPTEMWQALRAICDKHGILLISDEIQA 267 Query: 245 GAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPI 304 G RTGT+FA+E GVAPDL T AKS+AGG+P+AGV G+AE MDA+ PGGLGGTY G+P+ Sbjct: 268 GFARTGTWFAIEHSGVAPDLITCAKSMAGGYPVAGVIGRAEVMDALEPGGLGGTYGGNPV 327 Query: 305 ACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYP--IIGDVRGLGSMIAVE-VF 361 ACAAALA IE E E LL RS A+G+ + A +I + + D+RGLG+M+AVE V Sbjct: 328 ACAAALAAIEAIESEDLLARSTALGDTMRARFADIGARVAPFRMWDIRGLGAMLAVEFVT 387 Query: 362 EKGTHTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECF 421 + GT TP+ A V+A A ++GLILLSCG +GN +RI+VPLTA DA++++GLAI E Sbjct: 388 DFGTATPDVALTKSVIAHALKRGLILLSCGMHGNAVRIMVPLTASDAIIEEGLAIFEAAL 447 Query: 422 AE 423 A+ Sbjct: 448 AD 449 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: 653 Number of extensions: 29 Number of successful extensions: 3 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: 460 Length adjustment: 32 Effective length of query: 393 Effective length of database: 428 Effective search space: 168204 Effective search space used: 168204 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