Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate RR42_RS21370 RR42_RS21370 4-aminobutyrate aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Cup4G11:RR42_RS21370 Length = 420 Score = 375 bits (963), Expect = e-108 Identities = 197/390 (50%), Positives = 249/390 (63%), Gaps = 2/390 (0%) Query: 23 NAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLALME 82 N+E+WD +GKRYIDF GI VLN GH +P +VEA+Q Q R TH A+ P+ Y+ L E Sbjct: 31 NSEIWDVEGKRYIDFAAGIAVLNTGHRHPRLVEAMQRQLERFTHTAYQIVPYASYIELAE 90 Query: 83 QLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLATLNLNGK 142 +++Q P +GAEA ENA+K+AR ATG+ +IAF GGFHGRT+ + L GK Sbjct: 91 RINQRAPGRGAKKTAFFTTGAEAVENAIKIARAATGRPGVIAFSGGFHGRTMMGMALTGK 150 Query: 143 VAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAFIFEPVQGE 202 V PYK G PG V+H PYP A GV+ E ALKAM+ LF ++ + VAA IFEPVQGE Sbjct: 151 VVPYKVGFGPFPGEVFHAPYPCALHGVSVEDALKAMEHLFKADVDPKRVAAIIFEPVQGE 210 Query: 203 GGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAKSIA 262 GGF PAF +ALR CDE GIL++ DE+Q+GFGRTG+ FA + PDL +AKS+A Sbjct: 211 GGFNVAPPAFVKALRAICDEHGILLVADEVQTGFGRTGKLFAMEHYDVAPDLTTMAKSLA 270 Query: 263 GGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATWGERQEQAI 322 GGMPL AV GR E+M A GGLGGTY+GNP++ A+ALA L + E L G Q + Sbjct: 271 GGMPLSAVCGRAEVMDAPAPGGLGGTYAGNPLAVASALAVLDVLEGEQLIPRGAALGQRL 330 Query: 323 VSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARARGLLLMPSG 382 V+R E KA P I + G+GAM +EF ADG+P +V A +GLLL+ G Sbjct: 331 VARLEALKAR--VPQIAEIRGLGAMVAVEFRRADGAPDAEFTREVQNRALEQGLLLLSCG 388 Query: 383 KARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 ++IR L PLTI V+ EGLDIL L Sbjct: 389 VYGNVIRFLFPLTISDAVMNEGLDILADVL 418 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: 547 Number of extensions: 22 Number of successful extensions: 3 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: 420 Length adjustment: 32 Effective length of query: 384 Effective length of database: 388 Effective search space: 148992 Effective search space used: 148992 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