Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate PfGW456L13_4982 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4982 Length = 416 Score = 350 bits (899), Expect = e-101 Identities = 180/416 (43%), Positives = 259/416 (62%), Gaps = 4/416 (0%) Query: 12 REAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQL 71 R + + + +HP+ KNA V D +G+ +IDF GGI VLN GH HP+I+ A+ EQ Sbjct: 2 RSETISQSINIVHPVTLSHGKNAEVWDTDGKRYIDFVGGIGVLNLGHCHPRIVEAIREQA 61 Query: 72 NKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAG 131 +LTH F +EPY+EL + ++A +P + +L +G+EA ENA+KI R ATGR+ Sbjct: 62 TRLTHYAFNAAPHEPYLELMDCLSAFMPVGYPVSGMLTNSGAEAAENALKIVRGATGRSA 121 Query: 132 VIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERI 191 VIAF GA+HGRT+ TL L GKV PY +G++PG +F +P+ +GV+ +++ ++ER+ Sbjct: 122 VIAFDGAFHGRTLATLNLNGKVAPYKQKVGVLPGPVFHLPFPSRDNGVTCAEALKAMERL 181 Query: 192 FKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGT 251 F + + D+A I+EPVQGE GF EF + LR CD GI+LIADE+Q+G GRTG Sbjct: 182 FSVEIDVEDVACFIVEPVQGEAGFLAMDIEFAQALRKFCDDKGIVLIADEIQSGFGRTGE 241 Query: 252 FFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALA 311 FA ++G+ DL KSIAGG PL V G+ +D + GGLGGTY+G+PIACAAALA Sbjct: 242 RFAFSRLGIEPDLILLGKSIAGGVPLGAVVGRKSLLDNLPKGGLGGTYSGNPIACAAALA 301 Query: 312 VMEVFEEEHLLDRCKAVGERLVTGLKAIQAK--YPVIGEVRALGAMIAVELFENGDSHKP 369 ++ + +L E +V +A P +G + +GAM +EL N D P Sbjct: 302 TLDEMNDANLHAWGTQQEEAIVGRHATWRANNLTPYLGRLTGVGAMRGIELI-NADG-SP 359 Query: 370 NAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECFAEL 425 AA + Q++A ARD GL+L+ G +++R+L PLT A L++GL I+E C +L Sbjct: 360 AAAQLTQLLALARDAGLLLMPSGKSRHIIRLLAPLTIEAAVLEEGLDILEACLKKL 415 Lambda K H 0.320 0.137 0.394 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: 472 Number of extensions: 14 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: 425 Length of database: 416 Length adjustment: 32 Effective length of query: 393 Effective length of database: 384 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 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