Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate aminotransferase
Query= BRENDA::A0A140N9B6 (406 letters) >FitnessBrowser__BFirm:BPHYT_RS22435 Length = 427 Score = 216 bits (551), Expect = 8e-61 Identities = 141/393 (35%), Positives = 206/393 (52%), Gaps = 43/393 (10%) Query: 23 FIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEP 82 F R E + LWD +G+ +IDFA GIAV GH HP++ A+ +Q F HT Y P Sbjct: 24 FYAERAENAELWDVEGRRFIDFAAGIAVCNTGHRHPKILAAIRDQLDHFTHTA--YQIVP 81 Query: 83 V---LRLAKKLIDATFAD---RVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKN 136 + LA+KL + D + F +GAEA E A+K+AR + + G++AF Sbjct: 82 YASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARA------ATGRPGVIAFTG 135 Query: 137 AFHGRTLFTVSAGGQPA-YSQDFAPLPADIRHAAY----NDINSASAL----------ID 181 FHGRTL ++ G+ A Y F P P+D+ HA + + + +A +L ID Sbjct: 136 GFHGRTLMGMALTGKVAPYKIGFGPFPSDVFHAPFPNPLHGVTTADSLKAIEFLFKADID 195 Query: 182 DS-TCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMH 240 A+I EP+QGEGG PA F++ LR+LCN H LLI DEVQTG RTG+L+A H Sbjct: 196 PKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHH 255 Query: 241 YGVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELIN 300 Y V PDL+T AK+L GG P+ ++ + G G TY GNPLA A A VL++I+ Sbjct: 256 YDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAAHAVLDIID 315 Query: 301 TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLI--------GCVLNADYAGQAK 352 ++ D +L + ++VRG G ++ G +A++ K Sbjct: 316 EEKLCERATLLGDRVKAKLIALQSDVPQIADVRGPGGMVAVEFCKAGGTEPDAEF---TK 372 Query: 353 QISQEAAKAGVMVLIAG--GNVVRFAPALNVSE 383 ++ A + G+++L+ G NVVRF L + + Sbjct: 373 RVQTRALERGLLLLVCGVYSNVVRFLFPLTIQD 405 Lambda K H 0.319 0.135 0.406 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: 458 Number of extensions: 28 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: 406 Length of database: 427 Length adjustment: 31 Effective length of query: 375 Effective length of database: 396 Effective search space: 148500 Effective search space used: 148500 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