Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate H281DRAFT_01454 H281DRAFT_01454 carbohydrate ABC transporter substrate-binding protein, CUT1 family
Query= uniprot:A0A165KPY4 (416 letters) >FitnessBrowser__Burk376:H281DRAFT_01454 Length = 412 Score = 290 bits (743), Expect = 4e-83 Identities = 158/393 (40%), Positives = 230/393 (58%), Gaps = 9/393 (2%) Query: 24 EVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGGGDSAMTVLKSRVISGNPPSA 83 + V+H+WTSGGE+ ++ + G W D AVAG D A + +R++ G+PP+A Sbjct: 28 KANVIHWWTSGGESAAIRQFADAYNKAGGQWIDNAVAGA--DQARSTAINRIVGGDPPTA 85 Query: 84 AQ-TKGPAIQEWASEGVLANMDTLAKAEKWDELLPKVVADVMKYKGAYVAAPVNVHRVNW 142 AQ + +G+L N+D +A E W + P+ + D +K KG Y AAPV++H W Sbjct: 86 AQFNTSKQFHDLIDQGLLNNVDDVAAKENWSGVFPQSILDSIKVKGHYYAAPVDIHMPAW 145 Query: 143 MWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHGGQNWQDFTTFESVVLGVGG 202 + S A +KAG+ A P+++DEF A KL+AAG++P+A GGQ WQ+ TF++V+ VGG Sbjct: 146 FFYSKPAFQKAGITAEPQSYDEFIADLGKLRAAGVIPLAFGGQPWQEKITFDAVLADVGG 205 Query: 203 AKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPGRDWNLATAMLIQGKAGFQL 262 Y D A+ SD KK L F+R+ + D G+PGR+WN ATA++I GKAG Q+ Sbjct: 206 PDLYLKVYRDHDANAVKSDAFKKVLIAFKRLHDFVDAGSPGRNWNDATALVISGKAGVQI 265 Query: 263 MGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFILFKLKDAAAQKAQSDLASSI 322 MGDWAKGEF AA ++ GK+F C G + + D F+ K +A+ KAQ+ LA+ + Sbjct: 266 MGDWAKGEFSAAKQSAGKEFGCFPGFGPHSPYLVAGDVFVFPKSDNASTVKAQNLLATVM 325 Query: 323 MSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKDFVDTAKSGGLVPSAAHGMAIAPA 382 SP Q F+ KGSIP+R D CAK D ++ +P+ M ++P Sbjct: 326 TSPPAQVAFSAKKGSIPIRPDVDAGSLDICAKEGIAIMKDKSRQ---LPNPE--MLLSPD 380 Query: 383 TEGAIKDVVSQFWNDDKVSVADAMKKIAAAAKT 415 T+GA+ DVV+ FWN ++ SV DA K A A K+ Sbjct: 381 TQGALIDVVTNFWNKNQ-SVDDAQKAFAGALKS 412 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: 490 Number of extensions: 16 Number of successful extensions: 4 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: 412 Length adjustment: 31 Effective length of query: 385 Effective length of database: 381 Effective search space: 146685 Effective search space used: 146685 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 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