Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__azobra:AZOBR_RS25595 Length = 358 Score = 279 bits (713), Expect = 1e-79 Identities = 168/373 (45%), Positives = 221/373 (59%), Gaps = 23/373 (6%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA + LR V K++G + + ++L++ DGEF+ VGPSGCGKSTL+ IAGLE SGG Sbjct: 1 MAGVTLRGVRKSFGR--IEVIHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 + + ++ P R IAMVFQSYALYP M+ DN+AFGL + + I E V + Sbjct: 59 DLSIGGQRVNDRPPAARGIAMVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +LLQIE LL RKP LSGGQ+QRVA+GRA+ R P+++LFDEPLSNLDA LRV+MR E+ Sbjct: 119 RLLQIEDLLDRKPRDLSGGQRQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEIAK 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 + L+ T +YVTHDQ+EAMTL D++ V+ G ++Q GTP ++Y+ P N FVA FIGSP Sbjct: 179 LKADLRATMIYVTHDQVEAMTLADRIVVLNAGRVEQAGTPLELYHRPRNRFVAGFIGSPA 238 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQ-------DAGLEDREVILGIRPEQIIL 293 MNF+ + + L G R LP G+ A + LG+RPE + L Sbjct: 239 MNFLDVVSEG--------LTDGSVRVWLPGGVPLDIAVDGAAPAAGTPLTLGVRPEHVGL 290 Query: 294 ANGEANGLPTIRAEVQVTEPTGPDTLVFVNLND-TKVCCRLAPDVAPAVGETLTLQFDPA 352 A+G A L TI A E G +T L D ++ RL D A GE L L Sbjct: 291 ADGGAGLLATILA----VERLGGETHCHAALEDGQRLLVRLDGDRPVAAGERLRLNLRGE 346 Query: 353 KVLLFDAKTGERL 365 LF G+RL Sbjct: 347 TAHLF-GPDGQRL 358 Lambda K H 0.319 0.138 0.393 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: 428 Number of extensions: 23 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: 386 Length of database: 358 Length adjustment: 30 Effective length of query: 356 Effective length of database: 328 Effective search space: 116768 Effective search space used: 116768 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 (21.7 bits) S2: 49 (23.5 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