Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__HerbieS:HSERO_RS05420 Length = 426 Score = 361 bits (927), Expect = e-104 Identities = 188/391 (48%), Positives = 253/391 (64%), Gaps = 3/391 (0%) Query: 23 NAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLALME 82 NAE+WD +G+R+IDF GI VLN GH +P +++A++AQ + TH A+ P+ Y+ L E Sbjct: 35 NAELWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFTHTAYQIVPYASYVELAE 94 Query: 83 QLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLATLNLNGK 142 ++++ P +YP ++GAEA ENA+K+AR TG+ +IAF GGFHGRT+ + L GK Sbjct: 95 RINRLTPGNYPKKTAFFSTGAEAVENAIKIARAHTGRPGVIAFAGGFHGRTMMGMALTGK 154 Query: 143 VAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAFIFEPVQGE 202 VAPYK G PG V+H PYPSA G+T E AL+A+ LF ++ + VAA I EPVQGE Sbjct: 155 VAPYKLGFGPFPGDVFHAPYPSALHGITSEDALEAVKGLFKSDIEAKRVAAIILEPVQGE 214 Query: 203 GGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAKSIA 262 GGF A F + LR CDE GIL+I DE+QSG+GRTG+ FA + PDL+ +AKS+A Sbjct: 215 GGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRTGKLFAMEHYDVLPDLMTMAKSLA 274 Query: 263 GGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATWGERQEQAI 322 GGMPL AV GR E+M A GGLGGTY+GNP++ A+ALA L M +E L T G+R + Sbjct: 275 GGMPLSAVNGRAEIMDAPAPGGLGGTYAGNPLAIASALAVLDVMEEEQLVTRGQRLGDKL 334 Query: 323 VSRYERWKASGLSPYIGRLTGVGAMRGIEFAN-ADGSPAPAQLAKVMEAARARGLLLMPS 381 + ++S P I + GVGAM +EFA+ A G P KV + A GLLL+ Sbjct: 335 QEHLKELRSS--VPQIAEVRGVGAMVAVEFADPATGKPDAEYTKKVQQHALNNGLLLLTC 392 Query: 382 GKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 G ++IR L PLTI V++E L IL + + Sbjct: 393 GSYGNVIRFLFPLTIPDTVMDEALGILAKAI 423 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: 548 Number of extensions: 17 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: 426 Length adjustment: 32 Effective length of query: 384 Effective length of database: 394 Effective search space: 151296 Effective search space used: 151296 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