Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Pf1N1B4_1733 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1733 Length = 425 Score = 212 bits (539), Expect = 2e-59 Identities = 137/405 (33%), Positives = 212/405 (52%), Gaps = 44/405 (10%) Query: 16 PVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTG 75 P++A +A + + + D +G+E+IDFAGGIAV GH HP+++ A+TEQ K HT Sbjct: 25 PIFAESA------KNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTC 78 Query: 76 -NGYTNEPVLRLAKQL---IDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGI 131 EP + + +++ + FA + +G+EA E ++K+AR + ++G+ Sbjct: 79 FQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARA------ATGRAGV 132 Query: 132 VAFKNAFHGRTLFTVSAGGQPA-YSQDFAPLPPQIQHAIY-NDLDSAKALIDDNTC---- 185 +AF A+HGRT+ T+ G+ YS +P I A+Y N+L IDD+ Sbjct: 133 IAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS--IDDSIASIER 190 Query: 186 ------------AVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTG 233 A+I+EP+QGEGG A +F++ LR LCD H LLI DEVQTG GRTG Sbjct: 191 IFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTG 250 Query: 234 ELYAYMHYGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAG 293 +A GV DL + AK++ GGFP+ + + G G TY G+P+ACA A Sbjct: 251 TFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAAL 310 Query: 294 EVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVL---KDEYAGK 350 V +L+ K + L AI A+Y + E+R LG +I L D + Sbjct: 311 AVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFVDGDSHKPN 370 Query: 351 AKAISN---QAAEEGLMILIAG--ANVVRFAPALIISEDEVNSGL 390 A A+++ +A ++GL++L G NV+R L +++++ GL Sbjct: 371 AAAVASVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGL 415 Lambda K H 0.321 0.137 0.412 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: 445 Number of extensions: 23 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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