Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 3607949 Dshi_1357 ABC transporter related (RefSeq)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Dino:3607949 Length = 349 Score = 301 bits (770), Expect = 3e-86 Identities = 167/347 (48%), Positives = 221/347 (63%), Gaps = 19/347 (5%) Query: 15 GGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPAR 74 G V+ +DL I DGEFVV +GPSGCGKST+LRMI GLED S G + I G V D P Sbjct: 14 GDVQVIKGVDLEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRGAMLIDGVDVTDHPPA 73 Query: 75 ERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRA 134 +R + MVFQ+YALYPHMSV +N+ F L+ PAAEI +V AA+L LE L+R+P+ Sbjct: 74 KRGLTMVFQSYALYPHMSVRENMGFSLKTAGAPAAEIAEKVEAAAAVLKLEPYLDRRPKD 133 Query: 135 MSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHD 194 +SGGQ+QR AI R+I++ P+ FLFDEPLSNLDA LR ++R +I +LHQ L TT +YVTHD Sbjct: 134 LSGGQRQRVAIGRSIVRAPTAFLFDEPLSNLDAALRVEMRYEIAKLHQSLDTTMIYVTHD 193 Query: 195 QLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQL 254 Q+EAMTLADR+++++ G+I Q G+P ELY P NLF A FIG+P MN + T D Sbjct: 194 QVEAMTLADRIVVLEFGKIAQVGTPRELYETPANLFVAQFIGSPKMNVMPCTT---DAGR 250 Query: 255 FIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLT--CPVSVELVEIL 312 + +A + +G+R AV+L +RP+H+ P A T C V++VE L Sbjct: 251 YRLSAGRGGVFSGDR-------PAVQLGIRPEHI------TPGAPGTGACDGRVDVVEYL 297 Query: 313 GADALLTTRCGDQ-TLTALVPADRLPQPGATLTLALDQHELHVFDVE 358 GAD LL CG + +T V D PG + L+ + L FD + Sbjct: 298 GADTLLVLDCGPEGRVTVRVIGDTDLTPGDAVGLSFNPDRLSFFDTD 344 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: 359 Number of extensions: 17 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: 406 Length of database: 349 Length adjustment: 30 Effective length of query: 376 Effective length of database: 319 Effective search space: 119944 Effective search space used: 119944 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