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 Pf1N1B4_205 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)
Query= SwissProt::P50457 (421 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_205 Length = 470 Score = 227 bits (578), Expect = 7e-64 Identities = 145/412 (35%), Positives = 218/412 (52%), Gaps = 23/412 (5%) Query: 29 AENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFT--HTAYQIVPYESYV 86 A+ ++DVEG +ID AG L GH HP ++ A++Q L HT P + Sbjct: 56 AKGIYVEDVEGRSFIDCLAGAGTLALGHNHPVVIEAIQQVLTDELPLHTLDLTTPVKDQF 115 Query: 87 TLAEKINALAP-VSGQAKTAFF-TTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYMT 144 + + L P ++ +AK F TG +AVE A+K+ R TGR V++F GG+HG + Sbjct: 116 -VQDLFGLLPPALAAEAKIQFCGPTGTDAVEAALKLVRTATGRSTVLSFQGGYHGMSQGA 174 Query: 145 MALTGKVAPYKIGFGPFPGSVYHVPYPSDLH-------GISTQDSLDAIERLFKSDIEAK 197 ++L G + P K V +PYP D Q +L+ +E L Sbjct: 175 LSLMGSLGPKKPLGALLSSGVQFMPYPYDYRCPFGLGGAQGVQVNLNYLENLLNDPEAGV 234 Query: 198 QV-AAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHY 256 Q+ AA+I E VQGEGG A + + +RR+ ++ G+ +I DE+QSGFARTGK+FA +H Sbjct: 235 QLPAAVIVEAVQGEGGVIPADLDWLRGLRRITEKAGVALIVDEIQSGFARTGKMFAFEHA 294 Query: 257 ADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDK 316 PD++ M+K++ G +PL+ VV + +D PG GT+ GN +A+AA AV+ + + Sbjct: 295 GIIPDVVVMSKAIGGSLPLA-VVVYRDWLDTWLPGAHAGTFRGNQMAMAAGSAVMRYLTE 353 Query: 317 ESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPS--------A 368 +CE A +G+RL L + P + +RG G M+ VE DP TG P A Sbjct: 354 HKVCEHAAAMGERLSEHLHILQRDFPQLGDIRGRGLMLGVELVDP-TGAPDAQGHPPIFA 412 Query: 369 AIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420 +A +Q+ L +GL+L G +G V+RFL PL I A+ D I A++ Sbjct: 413 RLAPLVQRECLKRGLILELGGRHGGVVRFLPPLVITAAEIDRVADIFGRAMA 464 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: 480 Number of extensions: 23 Number of successful extensions: 5 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: 470 Length adjustment: 32 Effective length of query: 389 Effective length of database: 438 Effective search space: 170382 Effective search space used: 170382 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