Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_086510781.1 BZY95_RS15410 carbohydrate ABC transporter substrate-binding protein
Query= uniprot:A0A165KPY4 (416 letters) >NCBI__GCF_002151265.1:WP_086510781.1 Length = 422 Score = 462 bits (1189), Expect = e-135 Identities = 225/406 (55%), Positives = 293/406 (72%), Gaps = 2/406 (0%) Query: 9 AVAVGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGGGDSAM 68 A A + S A EVEVLH+WTSGGEA++ LK++M+ +G+ W DFAVAGGGG++AM Sbjct: 16 ATAAAASLTFSIQAAEVEVLHWWTSGGEARAANVLKELMEAEGYGWEDFAVAGGGGETAM 75 Query: 69 TVLKSRVISGNPPSAAQTKGPAIQEWASEGVLANMDTLAKAEKWDELLPKVVADVMKYKG 128 TVLKSR +SGNPPSAAQ KGP IQEW G+L +D +A+AE WDELLP VADVM++ G Sbjct: 76 TVLKSRAMSGNPPSAAQIKGPEIQEWGELGLLGELDEVAEAEGWDELLPPTVADVMRHNG 135 Query: 129 AYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHGGQNWQ 188 +YVA PVNVHRVNW+W + + L AGV MP T DE FAA + ++ AG +P+AHGGQ WQ Sbjct: 136 SYVAVPVNVHRVNWLWANPQVLAAAGV-EMPTTLDELFAAGEAIREAGYIPLAHGGQAWQ 194 Query: 189 DFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPGRDWNL 248 D T FESV+L GG +FYQ ALV+LD AL S+ M ++LETF+R++ D GRDWN+ Sbjct: 195 DATVFESVLLASGGTEFYQQALVELDPEALGSERMIEALETFKRLRELMDADMSGRDWNI 254 Query: 249 ATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFILFKLKD 308 AT+M+I+G AG QLMGDWAKGEF AAG G+++LCAAAPG+ +AFTFN+DS +F++ + Sbjct: 255 ATSMVIEGSAGMQLMGDWAKGEFTAAGLTAGEEYLCAAAPGTQDAFTFNIDSLAMFRV-E 313 Query: 309 AAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKDFVDTAKSGG 368 ++AQ LA ++ P FQE FNL KGSIP R M FD CA+ S DF TA+ GG Sbjct: 314 GEEREAQQALARLVLEPTFQEAFNLAKGSIPARPDLDMSGFDVCAQQSMDDFQRTAEEGG 373 Query: 369 LVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAK 414 LVPS AHGMA+ +GAI DVV+ ++N ++ +A +++ AA+ Sbjct: 374 LVPSMAHGMAVRADVQGAIFDVVTNYFNSRDMAAEEAARRMVNAAQ 419 Lambda K H 0.315 0.128 0.383 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: 560 Number of extensions: 28 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: 416 Length of database: 422 Length adjustment: 32 Effective length of query: 384 Effective length of database: 390 Effective search space: 149760 Effective search space used: 149760 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 (21.6 bits) S2: 50 (23.9 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