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 PfGW456L13_2301 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)
Query= SwissProt::P50457 (421 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2301 Length = 466 Score = 224 bits (571), Expect = 4e-63 Identities = 149/413 (36%), Positives = 220/413 (53%), Gaps = 25/413 (6%) Query: 29 AENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFT--HTAYQIVPYESYV 86 A+ ++DVEG +ID AG L GH HP ++ A++Q L HT P + Sbjct: 52 AKGIYVEDVEGRTFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTLDLTTPVKD-- 109 Query: 87 TLAEKINALAP--VSGQAKTAFF-TTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYM 143 + + L P ++ +AK F TG +AVE A+K+ R TGR VI+F GG+HG + Sbjct: 110 RFVQDLFGLLPPALAAEAKIQFCGPTGTDAVEAALKLVRTATGRSTVISFQGGYHGMSQG 169 Query: 144 TMALTGKVAPYKIGFGPFPGS-VYHVPYPSDLH-------GISTQDSLDAIERLFKSDIE 195 ++L G + P K G GS V +PYP D + +L +E L Sbjct: 170 ALSLMGSLGPKK-PLGALLGSGVQFMPYPYDYRCPFGLGGAQGVKANLSYLENLLNDPEA 228 Query: 196 AKQV-AAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMD 254 Q+ AA+I E VQGEGG A + + +RR+ ++ G+ +I DE+QSGFARTGK+FA + Sbjct: 229 GVQLPAAVIVEVVQGEGGVIPADLDWLRGVRRITEQAGVALIVDEIQSGFARTGKMFAFE 288 Query: 255 HYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNII 314 H PD++ M+K++ G +PL+ VV + +D PG GT+ GN +A+AA AV+ + Sbjct: 289 HAGIIPDVVVMSKAIGGSLPLA-VVVYRDWLDTWLPGAHAGTFRGNQMAMAAGCAVMRYL 347 Query: 315 DKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDP-----QTGEPS-- 367 + +CE A +G+RL L + P + +RG G M+ VE DP G P Sbjct: 348 VEHKVCEHAAAMGERLAEHLRILQRDFPQLGDIRGRGLMLGVELVDPTGALDAQGHPPAF 407 Query: 368 AAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420 A +A +Q+ L +GL+L G +G V+RFL PL I AQ D +I AL+ Sbjct: 408 ARLAPLVQRECLKRGLILELGGRHGAVVRFLPPLVITAAQIDRVAEIFGRALA 460 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: 464 Number of extensions: 21 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: 466 Length adjustment: 32 Effective length of query: 389 Effective length of database: 434 Effective search space: 168826 Effective search space used: 168826 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