Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate HSERO_RS16670 HSERO_RS16670 acetylornithine aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__HerbieS:HSERO_RS16670 Length = 400 Score = 179 bits (455), Expect = 1e-49 Identities = 132/416 (31%), Positives = 207/416 (49%), Gaps = 53/416 (12%) Query: 16 ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHY--AFNAAP 73 + + G + D +GKRY+D++ G V LGH + +A+ AQ+ +L + AF P Sbjct: 20 LVFTEGHGMWLTDHNGKRYLDYLQGWAVNTLGHAPQCIADALAAQSKKLINPSPAFYNEP 79 Query: 74 HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR---------GATGKRAIIA 124 L+ S F V + NSG EA E A+K+AR + + II Sbjct: 80 SIELAKLLTANSVFDRVFF------ANSGGEANEGAIKLARKWGKKNPAADGSARFEIIT 133 Query: 125 FDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSV 184 F FHGRTLAT++ +GK ++PG +P A ++ L SV Sbjct: 134 FKHSFHGRTLATMSASGKDGWDTMFAPQVPG------FPKA-----------VLNDLESV 176 Query: 185 ELAV-EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF 243 + + E A + EPVQGEGG + F Q LR E+ +L+I+DE+QSG GRTGQ F Sbjct: 177 KALIGEHTVAVMLEPVQGEGGVIPASKEFMQGLRSLTKEKNLLLIVDEVQSGMGRTGQLF 236 Query: 244 AFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303 A+ GIEPD++ LAK I GG+PL A++ R+E+ A G GGTY+GNP+ A +A + Sbjct: 237 AYQHSGIEPDIMTLAKGIGGGVPLAALLAREEI-ACFEAGEQGGTYNGNPLMTAVGVAVI 295 Query: 304 AQMTD----ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSP 359 ++ E++ G+ Q + E++ G G G +R ++ D P Sbjct: 296 KELLKPGFMESVRERGQYLRQRSLEISEKYGFEG-------ERGEGLLRALQLGR-DIGP 347 Query: 360 APAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 + A+ +E GLLL + +++R + L + E +++ +LE+ LA++ Sbjct: 348 QIVEAARNLEPV---GLLL--NSPRPNLLRFMPALNVTKEEIDQMFSMLEEVLAKI 398 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: 406 Number of extensions: 17 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: 400 Length adjustment: 31 Effective length of query: 385 Effective length of database: 369 Effective search space: 142065 Effective search space used: 142065 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 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