Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_028312613.1 H566_RS0118555 carbohydrate ABC transporter substrate-binding protein
Query= uniprot:A0A165KPY4 (416 letters) >NCBI__GCF_000482785.1:WP_028312613.1 Length = 418 Score = 526 bits (1355), Expect = e-154 Identities = 253/409 (61%), Positives = 316/409 (77%), Gaps = 2/409 (0%) Query: 8 AAVAVGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGGGDSA 67 A VA+ L A A +VEVLH+WTSGGEAKS ELKK+++ KG+ W+D AVAGGGGD+A Sbjct: 12 AFVALALLAPQ-VHAADVEVLHWWTSGGEAKSATELKKMVESKGNKWKDVAVAGGGGDNA 70 Query: 68 MTVLKSRVISGNPPSAAQTKGPAIQEWASEGVLANMDTLAKAEKWDELLPKVVADVMKYK 127 TV+KSR++SGNPP+AAQ KGP+IQEW +EGVLA++D +AKA WD LLP VVA++MKYK Sbjct: 71 ATVIKSRIVSGNPPTAAQIKGPSIQEWGAEGVLADIDDVAKAGNWDSLLPPVVANIMKYK 130 Query: 128 GAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHGGQNW 187 G YVA PVNVHRVNWMW + E KKAG A +P TW EF AA+K++ AG +PVAHGGQ W Sbjct: 131 GHYVAVPVNVHRVNWMWANPEVFKKAG-ATIPTTWAEFAVAAEKIQKAGFIPVAHGGQPW 189 Query: 188 QDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPGRDWN 247 QDFTTFES+ LGVGGA +Y+ A V+LD+ L T K+ ET ++ Y D + RDWN Sbjct: 190 QDFTTFESIALGVGGADYYKKAFVQLDDATLKGPTTVKAFETLAVVRKYIDKDSATRDWN 249 Query: 248 LATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFILFKLK 307 LAT M+I GKA Q MGDWAKGEF AAGK PGKD++C AAPG+ANAFTFN+DSF++F Sbjct: 250 LATGMVISGKAAMQFMGDWAKGEFTAAGKVPGKDYVCVAAPGTANAFTFNIDSFVMFDKA 309 Query: 308 DAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKDFVDTAKSG 367 A A+KA+ D AS++MSP FQEVFNLNKGSIPVR+G + KFDDCAK SA DF AK+G Sbjct: 310 GADAKKARGDFASAVMSPEFQEVFNLNKGSIPVRSGVDLSKFDDCAKKSAADFAADAKAG 369 Query: 368 GLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAKTK 416 L+P+ AH MA+ +T+GA++DVV+QF++ ++ A+A K+AAAAKTK Sbjct: 370 TLLPTIAHKMAVPESTQGAMQDVVTQFFHSSSMTPAEAATKLAAAAKTK 418 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: 654 Number of extensions: 37 Number of successful extensions: 2 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: 418 Length adjustment: 31 Effective length of query: 385 Effective length of database: 387 Effective search space: 148995 Effective search space used: 148995 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