Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF3586 Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type
Query= reanno::pseudo3_N2E3:AO353_11510 (425 letters) >FitnessBrowser__psRCH2:GFF3586 Length = 426 Score = 733 bits (1891), Expect = 0.0 Identities = 366/425 (86%), Positives = 395/425 (92%) Query: 1 MSKTNASLMKRREAAVPRGVGQIHPIFADHAKNSTVTDVEGREFIDFAGGIAVLNTGHLH 60 MSKTN SLM+RR AAVPRGVGQIHPIFADHAKNS+V DVEGREFIDFAGGIAVLNTGHLH Sbjct: 1 MSKTNESLMQRRVAAVPRGVGQIHPIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLH 60 Query: 61 PKVIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENSI 120 PK+I AV +QL+KLTHTCFQVLAYEPYVELCEKINA+VPGDFAKKTLLVTTGSEAVEN++ Sbjct: 61 PKIIKAVEDQLHKLTHTCFQVLAYEPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAV 120 Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKV PYSAGMGLMPGGIFRALYP ++GVS Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVAPYSAGMGLMPGGIFRALYPCAIYGVS 180 Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240 +DDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGF VAPK+FM RLRALCD+HGILLIAD Sbjct: 181 VDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFNVAPKDFMARLRALCDEHGILLIAD 240 Query: 241 EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300 EVQTGAGRTGTFFAMEQMGV ADLTTFAKS+ GGFP+AGVCGKAE MDAIAPGGLGGTYA Sbjct: 241 EVQTGAGRTGTFFAMEQMGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLGGTYA 300 Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360 G+P++CAAALAV+EVFEEE LLDRCKAV ERL TGLKAIQ K+ IGEVR LGAMIA+EL Sbjct: 301 GNPLSCAAALAVLEVFEEEKLLDRCKAVAERLTTGLKAIQTKHKEIGEVRGLGAMIAIEL 360 Query: 361 FENGDSHKPNAAAVAKVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAIMEE 420 FE+GD +P AA +++VA+ARDKGLILLSCGTY NVLRVLVPLTA DE LD+GLAI+ E Sbjct: 361 FEDGDHARPAAALTSQIVARARDKGLILLSCGTYYNVLRVLVPLTAEDELLDRGLAIIGE 420 Query: 421 CFSEL 425 CF EL Sbjct: 421 CFDEL 425 Lambda K H 0.320 0.137 0.395 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: 759 Number of extensions: 19 Number of successful extensions: 1 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: 426 Length adjustment: 32 Effective length of query: 393 Effective length of database: 394 Effective search space: 154842 Effective search space used: 154842 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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