Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF729 PGA1_c07440 ABC transporter, ATP binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Phaeo:GFF729 Length = 353 Score = 293 bits (751), Expect = 4e-84 Identities = 162/351 (46%), Positives = 225/351 (64%), Gaps = 14/351 (3%) Query: 15 GGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPAR 74 G V+H +DL I DGEF V +GPSGCGKST+LRMIAGLE+ S G + IG V L A Sbjct: 14 GDVQVIHDVDLSIDDGEFCVFVGPSGCGKSTLLRMIAGLEETSSGNIHIGDRDVTRLDAA 73 Query: 75 ERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRA 134 +R VAMVFQ+YALYPHM+V DN+ FGL+ P +I +V E + +L L+ L+RKP+A Sbjct: 74 DRGVAMVFQSYALYPHMTVEDNMGFGLKMNGHPKEKIREKVAEASRILKLDDYLKRKPKA 133 Query: 135 MSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHD 194 +SGGQ+QR AI RAI++ P VFLFDEPLSNLDA+LR +R +I RLH+ + T +YVTHD Sbjct: 134 LSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVDMRVEIARLHKEIGATMIYVTHD 193 Query: 195 QLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQL 254 Q+EAMTLAD++++++ GR+ Q GSP ELY P N F AGFIG+P+MNFL GTVQ DG + Sbjct: 194 QVEAMTLADKIVVLRAGRVEQVGSPMELYANPDNRFVAGFIGSPSMNFLEGTVQ-GDGVV 252 Query: 255 FIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILGA 314 ++R A + + V L +RP H+ + + + ++L E LG Sbjct: 253 VPALENRRVATS---VALPADGSKVLLGLRPQHLSV-------TAADSSLVLDLRERLGG 302 Query: 315 DA--LLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVESGENL 363 + L+T G++ + + LP+ G + L D + ++FD + + L Sbjct: 303 VSYDYLSTPTGEKLIVETRGDEALPE-GTAVALGFDDADAYIFDGATEQRL 352 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: 370 Number of extensions: 13 Number of successful extensions: 1 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: 353 Length adjustment: 30 Effective length of query: 376 Effective length of database: 323 Effective search space: 121448 Effective search space used: 121448 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