Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_011841343.1 RSPH17029_RS09880 aspartate aminotransferase family protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_4013 (425 letters) >NCBI__GCF_000015985.1:WP_011841343.1 Length = 436 Score = 166 bits (420), Expect = 1e-45 Identities = 126/412 (30%), Positives = 204/412 (49%), Gaps = 24/412 (5%) Query: 6 ADLMARRTAAVPRGVGQIH--PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKI 63 ADL+ARR A + + P+ + + D +G ++D +A L GH HP++ Sbjct: 22 ADLVARRQALLGPAYRLFYERPLHIVRGEGVWLYDADGTAYLDAYNNVASL--GHCHPRV 79 Query: 64 IAAVTEQLNKL-THTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKI 122 + AV Q +L THT + +E +EL E++ A +P + + TGSEA + A+++ Sbjct: 80 VEAVARQAGQLATHTRY---LHEGVLELAERLLATLPPELGH-AMFTCTGSEANDLALRL 135 Query: 123 ARAATGRAGVIAFTGAYHGRTMMTLGLT---GKVVPYSAGMGLMPGGIFRALYPNELHGV 179 A AATG GVI AYHG TM L+ G VP A + +P A P++ Sbjct: 136 AFAATGGTGVIVTENAYHGVTMGVAALSPSLGPGVPLGAHVRTVP-----APDPDKGADA 190 Query: 180 SIDDSIASIER-IFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLI 238 + ++A+ + ++ P AA+I++ V G + P + + A G L I Sbjct: 191 TFGAAVAAAAADLMRHGIRP---AALILDTVFSSDGVFTHPTDTLAPAAAAIRAAGGLFI 247 Query: 239 ADEVQTGAGRTG-TFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGG-LG 296 ADEVQ G GRTG + + GV D+ + K + G+P+A + + E + G Sbjct: 248 ADEVQPGFGRTGEAMWGFLRHGVVPDMVSMGKPMGNGYPVAALALRPELAERFGAGARYF 307 Query: 297 GTYAGSPIACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMI 356 T+ G+ +A AAALAV++ E E L VG + A L A+ + P +G VR G + Sbjct: 308 NTFGGNAVAAAAALAVLDTLEAEGLQAHALKVGGQFRADLSALSDRDPRLGAVRGAGLFL 367 Query: 357 AVELFENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPD 408 VE+ E +S P+A ++V R+ +++ + G +G+VL++ PL D Sbjct: 368 GVEVLE-PESRAPDARMATRIVNGLREARVLISATGPHGHVLKIRPPLVFSD 418 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: 432 Number of extensions: 30 Number of successful extensions: 6 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: 436 Length adjustment: 32 Effective length of query: 393 Effective length of database: 404 Effective search space: 158772 Effective search space used: 158772 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. 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