Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_25895 (367 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 240 bits (612), Expect = 5e-68 Identities = 141/351 (40%), Positives = 204/351 (58%), Gaps = 16/351 (4%) Query: 4 LKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTIELD 63 L++ L K F F+ + G+DL + F +G SGCGK+T LR+I+GLE TAG I L Sbjct: 19 LRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLG 78 Query: 64 GRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARILEL 123 +D+T+ P +R + VFQ YAL+PH+ + +N++F L G+ V+K V + ++EL Sbjct: 79 DQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGIRS--VKKPVEDMLDLVEL 136 Query: 124 GPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKEL 183 G + RKP QLSGGQ+QR+A+ RA++ P++ L DEPL LD LR QM++EL R+ E+ Sbjct: 137 GHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEV 196 Query: 184 QATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLK 243 T ++VTHDQ EAMT+AD + V+N GRIEQ+GSP ELY P FVA FLG + + Sbjct: 197 GLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLG--QSNLIA 254 Query: 244 GKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLA-----LPGDCTL 298 G V V +V G + LP + + G V LG+RPE + +A +P Sbjct: 255 GTVESVSGDVVQVAAH-GRSLALPAARCR-TTSGPVILGVRPEKVRIAKTEAEVPSGAN- 311 Query: 299 QVTADVSER--LGSDTFCHVLTASGEALTM--RIRGDLASRYGEQLSLHLD 345 +T V++ +G T V SGE L + + G R G ++ +H D Sbjct: 312 HLTGKVTDASFIGVSTQYLVELPSGEELAVFEQNTGQEIQRPGAEVVVHWD 362 Lambda K H 0.321 0.137 0.390 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: 342 Number of extensions: 20 Number of successful extensions: 3 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: 367 Length of database: 386 Length adjustment: 30 Effective length of query: 337 Effective length of database: 356 Effective search space: 119972 Effective search space used: 119972 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 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