Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__PS:Dsui_0023 Length = 396 Score = 179 bits (453), Expect = 2e-49 Identities = 134/400 (33%), Positives = 200/400 (50%), Gaps = 36/400 (9%) Query: 26 IFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAYE 85 +FA+ + + + D +G+ ++DF G AV GH HP I+ A+ Q KL + E Sbjct: 24 VFAEG-RGSWLVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGKLINPS-PAFYNE 81 Query: 86 PYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARA-----ATGRAGVIAFTGAYH 140 P ++L + A D + +TG+EA E A+K+AR G +I F G +H Sbjct: 82 PSLKLAAGLAAHSCFD---RVFFASTGAEANEGAIKLARKWGQKHKGGAHEIITFAGGFH 138 Query: 141 GRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKNDAEPRD 200 GRT+ T+ +GK + +PG F N+L DS+A++ Sbjct: 139 GRTLATMSASGKPGWDTLFAPQVPG--FPKAQLNDL------DSVAALIN--------ER 182 Query: 201 IAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGV 260 AI++EP+QGEGG A EF++ LR +CD G+LLI DEVQTG GRTG FA + G+ Sbjct: 183 TVAIMLEPIQGEGGVVPASAEFLQLLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHAGI 242 Query: 261 TADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEH 320 D+ T K I GG PL+ + K E + G GGTY G+P+ A AV+EV Sbjct: 243 EPDIMTLGKGIGGGVPLSALLAK-ESVCCFEAGDQGGTYNGNPLMTAVGAAVLEVLTAPG 301 Query: 321 LLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPNAAAVAQVVAK 380 L A GE L GL+ + + + GE R G + A+ L D P A+ + + Sbjct: 302 FLAEVAAKGEYLGAGLQRLSDRLGLRGE-RGQGLLRALLL---ADERGP---AIVEAARE 354 Query: 381 ARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420 +GL+L + ++LR + LT ++D+ LA +EE Sbjct: 355 RGPEGLLLNA--PRPHLLRFMPSLTVSREEIDQMLAWLEE 392 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: 431 Number of extensions: 25 Number of successful extensions: 5 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: 396 Length adjustment: 31 Effective length of query: 394 Effective length of database: 365 Effective search space: 143810 Effective search space used: 143810 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