Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate PP_4108 PP_4108 putative 4-aminobutyrate aminotransferase
Query= BRENDA::Q3ZCF5 (439 letters) >FitnessBrowser__Putida:PP_4108 Length = 416 Score = 180 bits (457), Expect = 7e-50 Identities = 131/409 (32%), Positives = 200/409 (48%), Gaps = 42/409 (10%) Query: 59 PVALERGKGIYVWDVEGRKYFDFLSAYSAVNQGHCHPKIVDALKSQVDKLTLTSRAFYNN 118 P+ L G+ VWD +G++Y DF+ +N GHC+P +V+A+++Q +LT AF Sbjct: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLT--HYAFNAA 72 Query: 119 VLGEYEEYVTKLFNYHKV------LPMNTGVEAGETACKLARKWGYTVKGIPKYKAKIVF 172 G Y + +L + V + N+G EA E A K+AR G +A I F Sbjct: 73 PHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR-------GATGKRAIIAF 125 Query: 173 AAGNFWGRTLSAISSSTDPTSYDGFGPFMPG-FEIIPYND----------LPALERA--- 218 G F GRTL+ ++ + Y +PG +PY L A++R Sbjct: 126 DGG-FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSV 184 Query: 219 -LQDPNVAAFMVEPIQGEAGVVVPDPGYLVGVRELCTQHQVLFIADEIQTGLARTGRWLA 277 L +VAAF+ EP+QGE G + DP + +R C + +L I DEIQ+G RTG+ A Sbjct: 185 ELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFA 244 Query: 278 IDHENVRPDIVLLGKALSGGLYPVSAVLCDDEIMLTIKPGEHGSTYGGNPLGCRVAIAAL 337 + PD++LL K+++GG+ P+ AV+ E+M + G G TY GNP+ C A+A+L Sbjct: 245 FPRLGIEPDLLLLAKSIAGGM-PLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303 Query: 338 EVLEEENLAENAEK--MGIILRNELMKLP--SDVVTTVRGKGLLNAIVIRETKDCDA--- 390 + +ENLA E+ I+ R E K S + + G G + I A Sbjct: 304 AQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQ 363 Query: 391 -WKVCLRLRDNGLLAKPT--HGDIIRFAPPLVIKEDEILEAVEIINKTI 436 KV R GLL P+ IIR PL I+ + + E ++I+ + + Sbjct: 364 LAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 Lambda K H 0.319 0.138 0.411 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: 402 Number of extensions: 23 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: 439 Length of database: 416 Length adjustment: 32 Effective length of query: 407 Effective length of database: 384 Effective search space: 156288 Effective search space used: 156288 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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