Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__azobra:AZOBR_RS25595 Length = 358 Score = 296 bits (757), Expect = 8e-85 Identities = 175/363 (48%), Positives = 221/363 (60%), Gaps = 20/363 (5%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + + + K + G V+H +DL + DGEFV +GPSGCGKST+LR+IAGLE+ SGG Sbjct: 1 MAGVTLRGVRKSF-GRIEVIHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGD 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 L IGG VND P R +AMVFQ+YALYPHM+ YDN+AFGL + I RVR A Sbjct: 60 LSIGGQRVNDRPPAARGIAMVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAAR 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 LL +E LL+RKPR +SGGQ+QR AI RAI++ P VFLFDEPLSNLDA LR Q+R +I +L Sbjct: 120 LLQIEDLLDRKPRDLSGGQRQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEIAKL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 LR T +YVTHDQ+EAMTLADR++++ GR+ QAG+P ELY PRN F AGFIG+PAM Sbjct: 180 KADLRATMIYVTHDQVEAMTLADRIVVLNAGRVEQAGTPLELYHRPRNRFVAGFIGSPAM 239 Query: 241 NFLSGTVQ-RQDGQLFIETAHQRWALTGERFSRLRHAMA------VKLAVRPDHVRIAGE 293 NFL + DG + + W G A + L VRP+HV +A Sbjct: 240 NFLDVVSEGLTDGSVRV------WLPGGVPLDIAVDGAAPAAGTPLTLGVRPEHVGLA-- 291 Query: 294 REPAASLTCPVSVELVEILGADALLTTRCGD-QTLTALVPADRLPQPGATLTLALDQHEL 352 + A L ++ VE LG + D Q L + DR G L L L Sbjct: 292 -DGGAGLL--ATILAVERLGGETHCHAALEDGQRLLVRLDGDRPVAAGERLRLNLRGETA 348 Query: 353 HVF 355 H+F Sbjct: 349 HLF 351 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: 454 Number of extensions: 24 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: 358 Length adjustment: 30 Effective length of query: 376 Effective length of database: 328 Effective search space: 123328 Effective search space used: 123328 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