Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate SMc02413 SMc02413 aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Smeli:SMc02413 Length = 437 Score = 241 bits (615), Expect = 3e-68 Identities = 141/408 (34%), Positives = 214/408 (52%), Gaps = 15/408 (3%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P + G G + DG DF++ G ++GHSHP + EA+ + S Sbjct: 22 PQAVVGGSGAYLTADDGRQLLDFSASWGAASLGHSHPAIREAVGRALSDQAGASYLSSAN 81 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 E ++LAEKL+ L P +V +G+SG++ANE ++V TGR + LAF+ A+HG T Sbjct: 82 EACVLLAEKLLSLVPERARGRVWFGHSGSDANETVARIVVAATGRPRILAFHGAYHGGT- 140 Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216 + S+ S Q G G+T +PYPN Y P+ + L +E Sbjct: 141 -IGSMGVSGHPAQQG--SRAEGLTLVPYPNSY-------AAGSPEAARDAALAHLERLFA 190 Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276 VPP E+ A F EPIQ +GG +VPP GFFKA++ +GIL+ DEV++G+GR+G+F Sbjct: 191 TEVPPEEVAAFFIEPIQSDGGMLVPPDGFFKAVEALCRRHGILIVSDEVKVGLGRSGRFN 250 Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHATTFGGNPVAIAAGIEVVE 336 A EH G+EPD++ FGK +GGGLP++ V+ I T GNPV AA + V++ Sbjct: 251 AFEHSGIEPDIVVFGKGLGGGLPISAVVGPEAIMNHSVAFSLQTVHGNPVCAAAALAVLQ 310 Query: 337 IVK--ELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELR 394 ++ L+ + G L + L+ ++ +IGD RG GLA +E+V ++E Sbjct: 311 TIERDHLILNADRSGKVLREALDRLTARHTLIGDVRGRGLALGIELVTDPASREPASRQA 370 Query: 395 DRIVKESAKRGLVL--LGCGDNSIRFIPPLIVTKEEIDVAMEIFEEAL 440 V + + GLVL +G N + PPL +T E + + + +AL Sbjct: 371 ALTVYRAFQLGLVLYYVGVQSNVLELTPPLTLTPAEAESGVAMLGQAL 418 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: 489 Number of extensions: 30 Number of successful extensions: 4 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: 437 Length adjustment: 32 Effective length of query: 413 Effective length of database: 405 Effective search space: 167265 Effective search space used: 167265 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 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