Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate AZOBR_RS19025 AZOBR_RS19025 acetylornithine aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__azobra:AZOBR_RS19025 Length = 389 Score = 185 bits (470), Expect = 2e-51 Identities = 139/407 (34%), Positives = 202/407 (49%), Gaps = 39/407 (9%) Query: 16 ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75 I G ++ TDG+R++DF G+ V LGH NP +VEA+ AQA +L H + N Sbjct: 14 IVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTS-NLFRVA 72 Query: 76 PYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGGF 129 +L ++L++ ++ TNSGAEA E K+ R G + II F+ F Sbjct: 73 GQESLAKRLTE---ATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQAF 129 Query: 130 HGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVE 189 HGRTLA ++ A ++++ + GP+ L L +V AV Sbjct: 130 HGRTLAAVS-----AAQQEKLIKGFGPLLD------------GFDLVPFGDLEAVRNAVT 172 Query: 190 DVAAFI-FEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248 D A I EP+QGEGG A F + LR CDE G+L+ +DEIQ G GRTG+ FA Sbjct: 173 DETAGICLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWA 232 Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308 GI PD++ +AK I GG PLGA + ++ + + G G TY GNP++ A A L ++ + Sbjct: 233 GITPDVMAVAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLE 292 Query: 309 ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVM 368 +R + R A + + G + G G M G+ A G V+ Sbjct: 293 PGFLDHVQRIGGLLQDRLAGLVAENPAVFKG-VRGKGLMLGLACGPAVGD--------VV 343 Query: 369 EAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 A RA GLL +P+G +++RLL PL I +EE + IL + EL Sbjct: 344 VALRANGLLSVPAGD--NVVRLLPPLNIGEAEVEEAVAILAKTAKEL 388 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: 454 Number of extensions: 20 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 416 Length of database: 389 Length adjustment: 31 Effective length of query: 385 Effective length of database: 358 Effective search space: 137830 Effective search space used: 137830 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