Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_011649926.1 RL_RS00545 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000009265.1:WP_011649926.1 Length = 426 Score = 257 bits (657), Expect = 4e-73 Identities = 160/424 (37%), Positives = 229/424 (54%), Gaps = 25/424 (5%) Query: 26 LAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEK 85 + MTTQ I +R E ++D +G + DFA+G+ V+N GH HPRV+ A+K Q ++ Sbjct: 18 VGMTTQ------IYADRAENAEIWDKEGRRYIDFAAGIAVLNTGHRHPRVIAAVKDQLDR 71 Query: 86 FTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFL 145 FTH YE+ + LAE+L L PGD E+K ++ +GAEA E A+K+ + TGR + Sbjct: 72 FTHTCHQVVPYESYVHLAERLNALLPGDFEKKTIFVTTGAEAVENAVKIARAATGRSAVI 131 Query: 146 AFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPG-VTHIPYPNPYRNTWGIDGYEEPDELT 204 AF FHGRT ++LT K V F MPG V HIP+P E Sbjct: 132 AFGGGFHGRTFMGMALT-GKVVPYKVGFGAMPGDVFHIPFP-----------VELHGVTA 179 Query: 205 NRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDE 264 ++ L +++ V P + AI EP+QGEGG+ P F KAL++ D++GILL DE Sbjct: 180 DQSLAALKKLFAADVDPQRVAAIIIEPVQGEGGFYSAPAAFMKALRELCDQHGILLIADE 239 Query: 265 VQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGG 323 VQ G RTG+ +A++H V PDL K++ GG PLA V RA I PG T+GG Sbjct: 240 VQTGFARTGRMFAMDHHEVAPDLTTMAKSLAGGFPLAAVTGRAAIMDAPGPGGLGGTYGG 299 Query: 324 NPVAIAAGIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIV 381 NP+ IAA V++++ ++L +G L + LE +E I D RG G AVE Sbjct: 300 NPLGIAAAHAVLDVIVDEDLCNRANLLGGRLKQRLESMRETVPEIVDIRGPGFMNAVEF- 358 Query: 382 KSKETKEKYPELRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEA 439 + T E +R+ + +GL+LL CG N IRF+ P+ + E A++I E + Sbjct: 359 NDRTTGLPSAEFANRVRLIALDKGLILLTCGVHGNVIRFLAPITIQDEIFGEALDILEAS 418 Query: 440 LKAA 443 + A Sbjct: 419 MLQA 422 Lambda K H 0.320 0.141 0.418 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: 484 Number of extensions: 26 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: 445 Length of database: 426 Length adjustment: 32 Effective length of query: 413 Effective length of database: 394 Effective search space: 162722 Effective search space used: 162722 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 (21.7 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