Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_076476008.1 BW971_RS02060 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_900156495.1:WP_076476008.1 Length = 452 Score = 258 bits (660), Expect = 2e-73 Identities = 161/443 (36%), Positives = 236/443 (53%), Gaps = 24/443 (5%) Query: 7 VKELPGPKAKEVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVI 66 V LPGP++ + +R + A+ +PI +G + DVDGN D SG+ V Sbjct: 16 VTPLPGPESSALAKR--RAAAVAAGVGSVVPIYAADADGGIIVDVDGNSLIDLGSGIAVT 73 Query: 67 NVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAE 126 VG S+P V +A+ QA FTH YE + +AEKL EL PGD E++ V NSGAE Sbjct: 74 GVGASNPAVADAVAAQAHHFTHTCFMVTPYEGYVAVAEKLNELTPGDHEKRSVLFNSGAE 133 Query: 127 ANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPN 186 A E A+K+ + TGR +AF HA+HGRT ++LTA + F P P + +P Sbjct: 134 AVENAVKVARLATGRDAIVAFDHAYHGRTNLTMALTAKTQPYKYNFGPFAPEIYRMPMSY 193 Query: 187 PYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFF 246 PYR+ G DG R + IE + + + EPIQGEGG++VP GF Sbjct: 194 PYRDDLGTDGV----SAAKRAIRQIE----TQIGGEAVAGLLIEPIQGEGGFIVPAPGFL 245 Query: 247 KALKKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHR 306 L ++A + G++ DEVQ G RTG ++A E G+ PD++ K I GG+PL+ + R Sbjct: 246 TTLAEWARDNGVVFIADEVQAGFCRTGTWFASEAEGIVPDIVTTAKGIAGGMPLSAITGR 305 Query: 307 ADITFDK--PGRHATTFGGNPVAIAAGIEVVEIVKEL-----LPHVQEVGDYLHKYLEEF 359 AD+ DK PG T+GGNPVA AA + + ++EL H++E+ L Sbjct: 306 ADL-LDKVHPGGLGGTYGGNPVACAAALATIAEMEELDLNARAHHIEEIA---LPRLRTL 361 Query: 360 KEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLL--GCGDNSIR 417 + +VIGD RG G A+EIV+ T P L ++ + + G+V+L G N IR Sbjct: 362 ADDLDVIGDVRGRGAMLAIEIVE-PGTDTPAPALAKKVAAAALEAGVVILVTGTFGNVIR 420 Query: 418 FIPPLIVTKEEIDVAMEIFEEAL 440 +PPL++ E + +++ E++L Sbjct: 421 LLPPLVIDDETLVDGIDVLEQSL 443 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: 531 Number of extensions: 24 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: 452 Length adjustment: 33 Effective length of query: 412 Effective length of database: 419 Effective search space: 172628 Effective search space used: 172628 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