Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate Ac3H11_909 Sulfate and thiosulfate import ATP-binding protein CysA (EC 3.6.3.25)
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_909 Length = 374 Score = 223 bits (567), Expect = 8e-63 Identities = 113/260 (43%), Positives = 166/260 (63%), Gaps = 6/260 (2%) Query: 4 IQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISID 63 I+ N+ K FG L+ + LDI GE + L+GPSGCGK+TLLR +AGLE+AD GTI Sbjct: 3 IEIRNVSKQFGDFQALRDVSLDIQSGELIALLGPSGCGKTTLLRIIAGLETADVGTIHFS 62 Query: 64 GKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLK----NLAAAEITKRVNEISE 119 G+ D+ + R++ VFQ YAL+ HMTV EN+ FGL++K + A+I K+V ++ + Sbjct: 63 GEDTTDVHVRERNVGFVFQHYALFRHMTVFENVAFGLRVKPRSERPSEAQIKKKVMDLLK 122 Query: 120 LLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRL 179 L+Q+ L +R P +LSGGQRQR+AL RAL+ + V+L DEP LDA +R ++R ++RL Sbjct: 123 LVQLDWLAERYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLRRL 182 Query: 180 HHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEM 239 H T I+VTHDQ EA + DR+ V+ G IEQ G+P +++ +P + F+ F+G ++ Sbjct: 183 HDELHVTSIFVTHDQEEALEVADRVVVINQGRIEQSGSPQQVWDQPASPFVYGFLG--DV 240 Query: 240 NFLEGAVLEKIPWPEARKAD 259 N G E + E + D Sbjct: 241 NLFHGRAHEGLVHLEGMQLD 260 Lambda K H 0.318 0.136 0.383 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: 282 Number of extensions: 10 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: 347 Length of database: 374 Length adjustment: 29 Effective length of query: 318 Effective length of database: 345 Effective search space: 109710 Effective search space used: 109710 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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