Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate PP_0214 PP_0214 4-aminobutyrate aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Putida:PP_0214 Length = 425 Score = 345 bits (884), Expect = 2e-99 Identities = 174/416 (41%), Positives = 260/416 (62%), Gaps = 11/416 (2%) Query: 5 SISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRL 64 ++ + + +HPI + +N+ V D +G+ IDF GGI VLN GH +P VV A+Q Q T++ Sbjct: 15 AVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKV 74 Query: 65 THYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIA 124 +H F + PY+ L E++++ VP + +L +G+EA ENA+K+AR ATG+ +IA Sbjct: 75 SHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARAATGRAGVIA 134 Query: 125 FDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSV 184 F GG+HGRT+ TL L GKV PY +G +PG ++ +PS G++ + A+ +++R+F Sbjct: 135 FTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKN 194 Query: 185 ELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFA 244 + D+AA I EPVQGEGGFL + LR CD+ GIL+I DE+Q+G GRTG FA Sbjct: 195 DAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFA 254 Query: 245 FPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLA 304 ++G+ PDL AKSIAGG PL V G+ E M A+ GGLGGTY+G+PI+CAAALA + Sbjct: 255 MEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVIE 314 Query: 305 QMTDENL----ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIE-FANADGSP 359 +E L GER + +++ P IG + G+G+M +E F +P Sbjct: 315 VFEEEKLLDRSKAVGERLTAGLREIQKKY------PIIGDVRGLGSMIAVEVFEKGTHTP 368 Query: 360 APAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 A + +V+ AR +GL+L+ G +++R+L PLT E +L++GL I+E+C AE+ Sbjct: 369 NAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECFAEI 424 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: 510 Number of extensions: 19 Number of successful extensions: 2 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: 425 Length adjustment: 32 Effective length of query: 384 Effective length of database: 393 Effective search space: 150912 Effective search space used: 150912 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