Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 3609758 Dshi_3141 ABC transporter related (RefSeq)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Dino:3609758 Length = 352 Score = 280 bits (717), Expect = 4e-80 Identities = 159/341 (46%), Positives = 219/341 (64%), Gaps = 12/341 (3%) Query: 25 LHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVAMVFQN 84 LH+ D EF+VLLGPSGCGK+T +RMIAGLED + G + IG +VND ++R+VAMVFQN Sbjct: 24 LHVRDEEFLVLLGPSGCGKTTTMRMIAGLEDPTDGEIWIGDRMVNDDLPKDRDVAMVFQN 83 Query: 85 YALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQQQRAA 144 Y LYPHM++++NIA+ LR AEI RV+ A + L L RKP+A+SGGQ+QR A Sbjct: 84 YGLYPHMTIFENIAYPLRVRGVDKAEIPPRVQRAAEQVELTKFLHRKPKALSGGQRQRVA 143 Query: 145 IARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAMTLADR 204 +ARAI++ P VFL DEPLSNLDAKLR +R ++K L + L+ TTVYVTHDQ+EAMTLADR Sbjct: 144 LARAIVRKPKVFLMDEPLSNLDAKLRVTMRAELKHLSRELQITTVYVTHDQIEAMTLADR 203 Query: 205 VILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIETAHQRWA 264 V +M+ G I Q G+P E+Y P NLF AGFIG+PAMN ++G+V +DG +F+ T R Sbjct: 204 VAVMKHGVIQQLGTPDEIYNDPANLFVAGFIGSPAMNLINGSV--EDG-MFVTTGGTRLV 260 Query: 265 LTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILGADALLTTRCGD 324 + A A+ L VR D +++ A V++ E G LLT + G Sbjct: 261 ----KVPSPDRARAI-LGVRADDMQV----HEAGQGDIDVTIYAFENTGESTLLTVQWGK 311 Query: 325 QTLTALVPADRLPQPGATLTLALDQHELHVFDVESGENLSL 365 Q + A + + ++L+ L++FD ++ E + + Sbjct: 312 QRVIARGDRHLRKEQDDVVGISLNTDHLYLFDPDTEERIRM 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: 392 Number of extensions: 18 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: 352 Length adjustment: 30 Effective length of query: 376 Effective length of database: 322 Effective search space: 121072 Effective search space used: 121072 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