Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Pf6N2E2_4013 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= BRENDA::A0A140N9B6 (406 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 Length = 425 Score = 214 bits (544), Expect = 5e-60 Identities = 142/399 (35%), Positives = 208/399 (52%), Gaps = 38/399 (9%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTG-NGYTN 80 P + + + D +G+E+IDFAGGIAV GH HP++ A+ EQ +K HT Sbjct: 25 PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAY 84 Query: 81 EPVLRLAKKL---IDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137 EP + L +K+ + FA + +G+EA E A+K+AR + ++G++AF A Sbjct: 85 EPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARA------ATGRAGVIAFTGA 138 Query: 138 FHGRTLFTVSAGGQPA-YSQDFAPLPADIRHAAY-NDINSASALIDDSTC---------- 185 +HGRT+ T+ G+ YS +P I A Y N+++ S IDDS Sbjct: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS--IDDSIASIERIFKNDA 196 Query: 186 ------AVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYM 239 A+I+EP+QGEGG A F++ LR LC++H LLI DEVQTG GRTG +A Sbjct: 197 EPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAME 256 Query: 240 HYGVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELI 299 GV DL T AK++ GGFP+ + E + G G TY G+P+A A A V+E+ Sbjct: 257 QMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVF 316 Query: 300 NTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVL--NAD-YAGQAKQISQ 356 +L+ K + V L I +Y + +VR LG +I L N D + A ++Q Sbjct: 317 EEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVELFENGDSHKPNAAAVAQ 376 Query: 357 EAAKA---GVMVLIAG--GNVVRFAPALNVSEEEVTTGL 390 AKA G+++L G GNV+R L +E++ GL Sbjct: 377 VVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGL 415 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: 449 Number of extensions: 20 Number of successful extensions: 4 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: 425 Length adjustment: 31 Effective length of query: 375 Effective length of database: 394 Effective search space: 147750 Effective search space used: 147750 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