Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3200 Length = 604 Score = 247 bits (631), Expect = 4e-70 Identities = 130/252 (51%), Positives = 171/252 (67%), Gaps = 12/252 (4%) Query: 13 GIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIV 72 G + + GV+K YG VLKD+ L V G V+ GPSGSGKST +R +N LE G I Sbjct: 354 GEVTIHGVSKRYGALEVLKDVTLTVLPGSVTVILGPSGSGKSTLLRSINHLERVDGGFIA 413 Query: 73 VDGVELTNDLKQIEAI-----------RREVGMVFQHFNLFPHLTILQNCTLAPMWVRKM 121 +DG EL + +A+ R +VGMVFQ+FNLFPHLT+L+N AP+ VRK+ Sbjct: 414 IDG-ELIGYRQDADALYELGENDILKRRVDVGMVFQNFNLFPHLTVLENIVEAPVTVRKL 472 Query: 122 PKRKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALD 181 + +AE +A+ L RV + ++AH YP QLSGGQQQRVAIARAL +KPK++LFDEPTSALD Sbjct: 473 ARAEAEALALELLARVGLSDKAHSYPRQLSGGQQQRVAIARALALKPKVLLFDEPTSALD 532 Query: 182 PEMVKEVLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQ 241 PE+V EVLD + LA G T++ VTHE+GFAR VA+ V+FM++G +VE P F P Sbjct: 533 PELVGEVLDVIKELARTGTTLVIVTHEIGFAREVADTVVFMEQGRVVETGTPAKVFSQPD 592 Query: 242 NDRTKLFLSQIL 253 + RT FL+++L Sbjct: 593 HPRTAAFLAKVL 604 Lambda K H 0.322 0.137 0.407 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: 335 Number of extensions: 8 Number of successful extensions: 2 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: 254 Length of database: 604 Length adjustment: 30 Effective length of query: 224 Effective length of database: 574 Effective search space: 128576 Effective search space used: 128576 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 (21.9 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