Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_061532689.1 CAter10_RS05910 sugar ABC transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >NCBI__GCF_001584165.1:WP_061532689.1 Length = 518 Score = 280 bits (715), Expect = 1e-79 Identities = 175/481 (36%), Positives = 271/481 (56%), Gaps = 17/481 (3%) Query: 20 VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79 VTKRF AL++ ++ GE HAL+G NGAGKSTL+ +L+G+ D+GE+R G Sbjct: 25 VTKRFPGVLALDNCQFNLLRGEVHALMGENGAGKSTLMKVLSGVYPKDSGEIRMDGRPVE 84 Query: 80 SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPL-RGGV-IDWQAMRRDARALLDH 137 R A + ++Q ++ LS A+N+FI R+P R GV +D A+ R A + + Sbjct: 85 IPNPRAAQALGIGIIHQELNLMNHLSAAQNIFIGREPRGRYGVFLDEDALNRQAAQIFER 144 Query: 138 WKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQ 197 ++ + G+L+V +Q+VEIA+ALS+ +R +I+DEPTA L+ EI LFR I +LQ Sbjct: 145 MRLQLDPRTLVGELTVAKQQMVEIAKALSFDSRVLIMDEPTAALNNAEIDDLFRIIRQLQ 204 Query: 198 REGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG---ERGGLA 254 GV ++ISH + E+ +I VTV+RD ++I + P P + +I M G + G Sbjct: 205 EHGVGIIYISHKMDELRQISNRVTVMRDGQYIATVPTVGTPIDTIIGMMVGRQLDNSGPE 264 Query: 255 VADAAARGALPADTAVALELKELT-GADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAIA 313 V D +A V LE+K LT GA + V+F++++GE++G G +GRT VA A+ Sbjct: 265 VPDTSAND-------VVLEVKGLTRGAAIKDVNFSLRKGEILGFAGLMGAGRTEVARAVF 317 Query: 314 GLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASM-TIARV 372 G A G I V G + ++AHGIG + +DR H GL V N M ++ + Sbjct: 318 GADAIDAGEILVHGVKVSIKSPRDAVAHGIGYLSEDRKHFGLATGLDVKTNVVMSSMDKF 377 Query: 373 LGK-FGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLV 431 L K + PA + Q + L I + V LSGGNQQK+V+A+ L + ++L Sbjct: 378 LTKGLFLDQPAIRET-AQGYVRQLSIKTPSIDQPVRLLSGGNQQKIVIAKWLLRDCDILF 436 Query: 432 LIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAEFP 490 +PT G+D+ +K + +++ + +GKA++++S EL + LR R+LVM GR+ E Sbjct: 437 FDEPTRGIDIGAKNEIYKLLNALAAQGKAIVMISSELPEVLRMSHRILVMCEGRITGELA 496 Query: 491 A 491 A Sbjct: 497 A 497 Lambda K H 0.318 0.134 0.377 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: 546 Number of extensions: 28 Number of successful extensions: 9 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: 510 Length of database: 518 Length adjustment: 35 Effective length of query: 475 Effective length of database: 483 Effective search space: 229425 Effective search space used: 229425 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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