Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__psRCH2:GFF857 Length = 371 Score = 296 bits (757), Expect = 9e-85 Identities = 169/364 (46%), Positives = 222/364 (60%), Gaps = 9/364 (2%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + + + K Y G P H +DL I DGEFVV +GPSGCGKST+LR+IAGLEDI+ G Sbjct: 1 MASVTLRDICKSYDGTPITRH-IDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGD 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 L I VNDLP ++R+V MVFQ+YALYPHM+V +N+AFGL+ EI RRV VA Sbjct: 60 LLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAE 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L L+ LLERKP+ +SGGQ+QR AI R +++ P VFLFDEPLSNLDA LR Q+R +I RL Sbjct: 120 ILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 HQR+R+T +YVTHDQ+EAMTLAD+++++ G I Q G P LY YP+N F AGF+G+P M Sbjct: 180 HQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQM 239 Query: 241 NFLS-GTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAAS 299 NF+ + + IE S + + L +RP+H + E A Sbjct: 240 NFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDE----AD 295 Query: 300 LTCPVSVELVEILGADAL--LTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDV 357 T + + E LG L LT +T V + G T L + H+F Sbjct: 296 FTFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFR- 354 Query: 358 ESGE 361 E+GE Sbjct: 355 ENGE 358 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: 397 Number of extensions: 17 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: 371 Length adjustment: 30 Effective length of query: 376 Effective length of database: 341 Effective search space: 128216 Effective search space used: 128216 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