Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate PfGW456L13_2301 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2301 Length = 466 Score = 221 bits (564), Expect = 3e-62 Identities = 142/425 (33%), Positives = 222/425 (52%), Gaps = 18/425 (4%) Query: 33 PENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLT 92 P +P+ ++R +GI V DV+G F D +G G + +GH+HP V+EAI++ Sbjct: 42 PRRIPLALKRAKGIYVEDVEGRTFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTL 101 Query: 93 DFFYENAIILAEKLIELAPGDI--ERKVVY-GNSGAEANEAAMKLVKYGTGRKQFLAFYH 149 D + L L P + E K+ + G +G +A EAA+KLV+ TGR ++F Sbjct: 102 DLTTPVKDRFVQDLFGLLPPALAAEAKIQFCGPTGTDAVEAALKLVRTATGRSTVISFQG 161 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209 +HG +Q LSL S ++ GV +PYP YR +G+ G + L Sbjct: 162 GYHGMSQGALSLMGSLGPKKPLGALLGSGVQFMPYPYDYRCPFGLGGAQG----VKANLS 217 Query: 210 FIEEYVFRHVPPHEI-GAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMG 268 ++E + ++ A+ E +QGEGG + + + +++ ++ G+ L DE+Q G Sbjct: 218 YLENLLNDPEAGVQLPAAVIVEVVQGEGGVIPADLDWLRGVRRITEQAGVALIVDEIQSG 277 Query: 269 IGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHATTFGGNPVAI 328 RTGK +A EH G+ PD++ KAIGG LPLA V++R + PG HA TF GN +A+ Sbjct: 278 FARTGKMFAFEHAGIIPDVVVMSKAIGGSLPLAVVVYRDWLDTWLPGAHAGTFRGNQMAM 337 Query: 329 AAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIV----- 381 AAG V+ + E + H +G+ L ++L + + +GD RG GL VE+V Sbjct: 338 AAGCAVMRYLVEHKVCEHAAAMGERLAEHLRILQRDFPQLGDIRGRGLMLGVELVDPTGA 397 Query: 382 -KSKETKEKYPELRDRIVKESAKRGLVLLGCGDNS--IRFIPPLIVTKEEIDVAMEIFEE 438 ++ + L + +E KRGL+L G + +RF+PPL++T +ID EIF Sbjct: 398 LDAQGHPPAFARLAPLVQRECLKRGLILELGGRHGAVVRFLPPLVITAAQIDRVAEIFGR 457 Query: 439 ALKAA 443 AL AA Sbjct: 458 ALAAA 462 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: 517 Number of extensions: 30 Number of successful extensions: 6 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: 466 Length adjustment: 33 Effective length of query: 412 Effective length of database: 433 Effective search space: 178396 Effective search space used: 178396 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