Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate PP_4223 PP_4223 diaminobutyrate-2-oxoglutarate transaminase
Query= SwissProt::P50457 (421 letters) >FitnessBrowser__Putida:PP_4223 Length = 452 Score = 218 bits (556), Expect = 2e-61 Identities = 146/403 (36%), Positives = 216/403 (53%), Gaps = 27/403 (6%) Query: 29 AENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFT--HTAYQIVPYESYV 86 A ++DVEG ++ID AG L GH HP +V A+++ L HT P + Sbjct: 38 ARGIHVEDVEGRQFIDCLAGAGTLALGHNHPVVVEAIQRVLADELPLHTLDLTTPVKD-- 95 Query: 87 TLAEKINALAP--VSGQAKTAFF-TTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYM 143 + + + P + +AK F TG +AVE A+K+ R TGR V+AF G +HG + Sbjct: 96 RFVQDLFGILPEALRREAKVQFCGPTGTDAVEAALKLVRTATGRSTVLAFQGAYHGMSQG 155 Query: 144 TMALTGKVAPYKIGFGPFPGS-VYHVPYPSDLH---GISTQDSLDA----IERLFKSDIE 195 + L G P K G G+ V +PYP D G+ + + A +E L Sbjct: 156 ALNLMGSHGP-KQPLGALLGNGVQFMPYPYDYRCPFGLGGEAGVKANLHYLENLLLDPES 214 Query: 196 AKQV-AAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMD 254 + AA+I E VQGEGG A E + +RR+ ++ G+ +I DE+QSGFARTG++FA + Sbjct: 215 GVPLPAAVILEVVQGEGGVVPADIEWLKGVRRITEQAGVALIVDEIQSGFARTGRMFAFE 274 Query: 255 HYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNII 314 H PD++T++K++ G +PL+ VV + +D PG GT+ GN +A+AA AV+N + Sbjct: 275 HAGIVPDVVTLSKAIGGSLPLA-VVVYRDWLDTWKPGAHAGTFRGNQMAMAAGSAVINYL 333 Query: 315 DKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAA----- 369 + L E A +GQRL+ L + P + +RG G M+ VE DPQ G+P A Sbjct: 334 VEHRLAEHAEAMGQRLRGHLQRLQRDYPQLGDIRGRGLMLGVELVDPQ-GQPDALGHPPA 392 Query: 370 ---IAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFD 409 +A K+Q+ L +GL+L G +G V+RFL PL I Q D Sbjct: 393 NRDLAPKVQRECLKRGLILELGGRHGAVVRFLPPLIISAEQID 435 Lambda K H 0.319 0.134 0.388 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: 504 Number of extensions: 27 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: 421 Length of database: 452 Length adjustment: 32 Effective length of query: 389 Effective length of database: 420 Effective search space: 163380 Effective search space used: 163380 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 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