Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate PfGW456L13_494 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__pseudo13_GW456_L13:PfGW456L13_494 Length = 425 Score = 211 bits (538), Expect = 2e-59 Identities = 135/403 (33%), Positives = 213/403 (52%), Gaps = 40/403 (9%) Query: 16 PVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTG 75 P++A +A + + + D +G+E+IDFAGGIAV GH HP+++ A+TEQ K HT Sbjct: 25 PIFADSA------KNATVTDVEGREFIDFAGGIAVLNTGHVHPKVIAAVTEQLNKLTHTC 78 Query: 76 -NGYTNEPVLRLAKQL---IDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGI 131 EP + + +++ + FA + +G+EA E ++K+AR + ++G+ Sbjct: 79 FQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARA------ATGRAGV 132 Query: 132 VAFKNAFHGRTLFTVSAGGQPA-YSQDFAPLPPQIQHAIYND------LDSAKALID--- 181 +AF A+HGRT+ T+ G+ YS +P I A+Y + +D + A I+ Sbjct: 133 IAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIF 192 Query: 182 ------DNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGEL 235 + A+I+EP+QGEGG A +F++ LR LCD H LLI DEVQTG GRTG Sbjct: 193 KNDAEPKDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTF 252 Query: 236 YAYMHYGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEV 295 +A GV DL + AK++ GGFP+ + + G G TY G+P+ACA A V Sbjct: 253 FAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAV 312 Query: 296 FATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVL---KDEYAGKAK 352 +L+ K + L AI A+Y + E+R LG +I L D + A Sbjct: 313 MEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPNAA 372 Query: 353 AISN---QAAEEGLMILIAG--ANVVRFAPALIISEDEVNSGL 390 A+++ +A ++GL++L G NV+R L +++++ GL Sbjct: 373 AVASVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGL 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: 447 Number of extensions: 22 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