Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate Pf1N1B4_1045 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1045 Length = 416 Score = 358 bits (918), Expect = e-103 Identities = 180/412 (43%), Positives = 263/412 (63%), Gaps = 4/412 (0%) Query: 16 VPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLT 75 + R + +HP+ KNA V D +G+ +IDF GGI VLN GH HP+I+ A+ EQ +LT Sbjct: 6 ISRSINIVHPVTLSHGKNAEVWDTDGKRYIDFVGGIGVLNLGHCHPRIVEAIREQATRLT 65 Query: 76 HTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAF 135 H F + PY+EL +++ A +P D+ +L +G+EA ENA+KI R ATGR VIAF Sbjct: 66 HYAFNAAPHAPYLELMDRLTAFIPVDYPVSGMLTNSGAEAAENALKIVRGATGRTAVIAF 125 Query: 136 TGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKND 195 GA+HGRT+ TL L GKV PY +G++PG +F +P++ + V+ +++ +++R+F + Sbjct: 126 DGAFHGRTLATLNLNGKVAPYKQKVGVLPGPVFHLPFPSKDNDVTCAEALKAMDRLFSVE 185 Query: 196 AEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAM 255 + D+A I+EPVQGE GF EF + LR CD GILLIADE+Q+G GRTG FA Sbjct: 186 IDVDDVACFIVEPVQGEAGFLAMDVEFAQALRRFCDDKGILLIADEIQSGFGRTGQRFAF 245 Query: 256 EQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEV 315 ++G+ DL KSIAGG PL V G+ +D + GGLGGTY+G+PIACAAALA ++ Sbjct: 246 SRLGIEPDLILLGKSIAGGVPLGAVVGRKSLLDNLPKGGLGGTYSGNPIACAAALATLDE 305 Query: 316 FEEEHLLDRCKAVGERLVTGLKAIQAK--YPVIGEVRALGAMIAVELFENGDSHKPNAAA 373 + HL E +V+ ++ +A+ P +G + +GAM +EL N D P +A Sbjct: 306 MTDAHLHAWGVQQEEAIVSRYESWRARELSPYLGRLTGVGAMRGIELI-NADG-TPASAQ 363 Query: 374 VAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECFAEL 425 + Q++A ARD GL+L+ G +++R+L PLT+ A L++GL I+E C A+L Sbjct: 364 LTQLLALARDSGLLLMPSGKSRHIIRLLAPLTTEAAVLEEGLDILEACLAKL 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: 464 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