Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Phaeo:GFF2829 Length = 440 Score = 152 bits (385), Expect = 1e-41 Identities = 132/422 (31%), Positives = 195/422 (46%), Gaps = 43/422 (10%) Query: 28 DTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLALMEQLSQF 87 D +GKRY+D GG V LGH + V+ A+Q Q +L P AL + L Sbjct: 26 DANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLAFAHTGFLTSEPAEALADLLISQ 85 Query: 88 VPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGGFHGRTLATLNLNG 141 P + G+EA E A+K+AR G T +R +IA +HG TL L G Sbjct: 86 APGDLHRV-YFVSGGSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHGNTLGALAAGG 144 Query: 142 KVAPYKQRVGELPGPVYHLP--YPSADTG---VTCEQALKAMDRLFS--VELAVEDVAAF 194 A +Q+ L + H+ Y D G + + + L + + L E V AF Sbjct: 145 N-AWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDYGQRVANELEAEILRLGPETVMAF 203 Query: 195 IFEPVQGE-GGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253 + EPV G G + + + +R CD+ G+L+I+DE+ G GRTG FA G+ PD Sbjct: 204 MAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTGHLFACEADGVAPD 263 Query: 254 LLLLAKSI-AGGMPLGAVVGRKELMAALPKGG----LGGTYSGNPISCAAALASLAQMTD 308 +L +AK + AG P+GA++ +++ A+ G G TY G+P++ AA LA + + D Sbjct: 264 ILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVATAAGLAVVRALLD 323 Query: 309 ENL----ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQ- 363 L A GE A+V+R+ G P++G L G G RGIE S P Sbjct: 324 RGLVQRSAEMGETLHAALVARF------GQHPHVGDLRGRGLFRGIELVADRESKTPFDP 377 Query: 364 ----LAKVMEAARARGLLLMPSGKAR------HIIRLLAPLTIEAEVLEEGLDILEQCLA 413 K+ +AA GL+ P R HI+ L P + + + E D LE L Sbjct: 378 GLGIAGKLKKAAFEAGLICYPMAGTRDGRNGDHIL-LAPPFILSEDQIGEITDKLEVALD 436 Query: 414 EL 415 ++ Sbjct: 437 QV 438 Lambda K H 0.320 0.137 0.402 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: 475 Number of extensions: 24 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: 416 Length of database: 440 Length adjustment: 32 Effective length of query: 384 Effective length of database: 408 Effective search space: 156672 Effective search space used: 156672 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