Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate 3607384 Dshi_0798 acetylornithine and succinylornithine aminotransferase (RefSeq)
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Dino:3607384 Length = 393 Score = 181 bits (458), Expect = 4e-50 Identities = 131/407 (32%), Positives = 195/407 (47%), Gaps = 41/407 (10%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA-FNAAP 73 P++ G A + + DG+R++D GI V LGH +P +V A+ QA L H + P Sbjct: 13 PLSFVKGEGAWLIEADGRRFLDLGAGIAVNALGHAHPRLVAALTDQAQALWHVSNLYQIP 72 Query: 74 HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDG 127 LA M F + TNSG E+ E A+K+ R G + I+ F+G Sbjct: 73 AQQKLAEMLVAETFADTVF-----FTNSGTESCELAVKMVRKHFHDAGQPERVEILTFEG 127 Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187 FHGR+ A + G K LPG HLP+ + + +++ A Sbjct: 128 SFHGRSSAGIAAAGSEKMTKGFGPLLPG-FRHLPFGNHE----------------ALQSA 170 Query: 188 VED-VAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246 V D AA + EPVQGEGG AL A + LR CD+ GIL+I+DE+Q G GRTG+ FA Sbjct: 171 VNDRTAAIMVEPVQGEGGIRALPDACLKGLRDLCDQHGILMILDEVQCGVGRTGRLFAHE 230 Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306 G+ PD++++AK I GG PLGAV+ + + + G G TY GNP+ CA A L + Sbjct: 231 WAGVSPDIMMVAKGIGGGFPLGAVLATADAASGMTAGTHGSTYGGNPLGCAVGCAVLETV 290 Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAK 366 + R++ ++ + + + G G M G+ A Sbjct: 291 CADGFLE-EVRRKAGLMRQALEGLVAEFPGVFAEVRGAGLMLGL--------VCRAPNTD 341 Query: 367 VMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLA 413 V++A +L++P+ A +++RLL PLTI + E L L + A Sbjct: 342 VVQAGYGAEVLVVPA--AENVVRLLPPLTITDAEIREALARLRKAAA 386 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: 410 Number of extensions: 22 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: 416 Length of database: 393 Length adjustment: 31 Effective length of query: 385 Effective length of database: 362 Effective search space: 139370 Effective search space used: 139370 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: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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