Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Miya:8500851 Length = 354 Score = 209 bits (532), Expect = 1e-58 Identities = 118/285 (41%), Positives = 169/285 (59%), Gaps = 9/285 (3%) Query: 15 GGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVND---- 70 GG + L+L IG GE +LGPSGCGK+T LRM+AG ED+ G + +G +++ Sbjct: 14 GGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEIHVGDRLLSARRNN 73 Query: 71 --LPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALL 128 LP +R+ MVFQ +A++PH+SVY+N+AF LR + AAEIDRR RE +L + Sbjct: 74 YYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRRTREALHHTSLADVA 133 Query: 129 ERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTT 188 ++ P +SGG +QR A+ARA+ P V L DEPLS+LD LR ++R +IK L + + Sbjct: 134 QKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMRFEIKDLQRTFGFSI 193 Query: 189 VYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQ 248 +YVTHDQ EAM L+DR+++M++G + Q G+P ++Y P N F GFIG NFL + Sbjct: 194 LYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFGFIG--LSNFLDVNL- 250 Query: 249 RQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGE 293 +G + + R +RL A LA RP + E Sbjct: 251 TPEGLVRVNGGDARVTPATPPSARLVSAGRAALASRPSEIDFTAE 295 Lambda K H 0.321 0.137 0.403 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: 352 Number of extensions: 13 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: 406 Length of database: 354 Length adjustment: 30 Effective length of query: 376 Effective length of database: 324 Effective search space: 121824 Effective search space used: 121824 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