Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein
Query= reanno::pseudo3_N2E3:AO353_11510 (425 letters) >FitnessBrowser__Koxy:BWI76_RS11670 Length = 406 Score = 213 bits (541), Expect = 1e-59 Identities = 140/406 (34%), Positives = 210/406 (51%), Gaps = 46/406 (11%) Query: 25 PIFADHA------KNSTVTDVEGREFIDFAGGIAVLNTGHLHPKVIAAVTEQLNKLTHTC 78 P++A A + S + D +G+E+IDFAGGIAV GH HP+++ A+TEQ K HT Sbjct: 16 PVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTG 75 Query: 79 FQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARA------ATGRAGV 132 EP + L +++ + FA + +G+EA E ++K+AR + ++G+ Sbjct: 76 -NGYTNEPVLRLAKQL---IDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGI 131 Query: 133 IAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS--IDDSIASIER 190 +AF A+HGRT+ T+ G+ YS +P I A+Y N+L IDD+ Sbjct: 132 VAFKNAFHGRTLFTVSAGGQPA-YSQDFAPLPPQIQHAIY-NDLDSAKALIDDNTC---- 185 Query: 191 IFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTG 250 A+I+EP+QGEGG A +F++ LR LCD H LLI DEVQTG GRTG Sbjct: 186 ------------AVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTG 233 Query: 251 TFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAAL 310 +A GV DL + AK++ GGFP+ + + G G TY G+P+ACA A Sbjct: 234 ELYAYMHYGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAG 293 Query: 311 AVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPN 370 V +L+ K + L AI A+Y + E+R LG +I L K Sbjct: 294 EVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVL-------KDE 346 Query: 371 AAAVAKVVA-KARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGL 415 A AK ++ +A ++GL++L G NV+R L +++++ GL Sbjct: 347 YAGKAKAISNQAAEEGLMILIAG--ANVVRFAPALIISEDEVNSGL 390 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: 436 Number of extensions: 21 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: 425 Length of database: 406 Length adjustment: 31 Effective length of query: 394 Effective length of database: 375 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