Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate BPHYT_RS29190 BPHYT_RS29190 sugar ABC transporter substrate-binding protein
Query= uniprot:A0A165KPY4 (416 letters) >FitnessBrowser__BFirm:BPHYT_RS29190 Length = 412 Score = 298 bits (762), Expect = 3e-85 Identities = 164/410 (40%), Positives = 238/410 (58%), Gaps = 10/410 (2%) Query: 7 IAAVAVGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGGGDS 66 +AA+A+ A + V+H+WTSGGE+ ++ + G W D AVAG D Sbjct: 12 VAALAL-YGVVAQAEPLKANVIHWWTSGGESAAIRQFADAYNKAGGQWVDNAVAGA--DQ 68 Query: 67 AMTVLKSRVISGNPPSAAQ-TKGPAIQEWASEGVLANMDTLAKAEKWDELLPKVVADVMK 125 A + +R++ G+PP+AAQ + +G+L N+D +A E W+ + P+ + D +K Sbjct: 69 ARSTAINRIVGGDPPTAAQFNTSKQFHDLIDQGLLNNVDDVAAKENWNGVFPQSIIDSIK 128 Query: 126 YKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHGGQ 185 KG Y AAPV++H W + S +KAG+A PK++DEF A KLK AG++P+A GGQ Sbjct: 129 VKGHYYAAPVDIHMPAWFFYSKPVFQKAGIAGEPKSYDEFIADLGKLKTAGVIPLALGGQ 188 Query: 186 NWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPGRD 245 WQ+ TF++V+ VGG Y D A+ SD KK L +F+R+ + DPG+PGR+ Sbjct: 189 PWQEKITFDAVLADVGGPDLYMKVYRDRDMNAVKSDAFKKVLASFKRLHDFVDPGSPGRN 248 Query: 246 WNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFILFK 305 WN ATA++I GKAG Q+MGDWAKGEF AA ++ GKDF C G + + D F+ K Sbjct: 249 WNDATALVISGKAGVQIMGDWAKGEFSAANQSAGKDFGCFPGFGPHSPYLVAGDVFVFPK 308 Query: 306 LKDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKDFVDTAK 365 + KAQ+ LA+ + SPA Q F+ KGSIP+R D CAK D ++ Sbjct: 309 TDNPTTIKAQNLLATVMTSPAAQVAFSAKKGSIPIRPDVDGSSLDICAKEGIAIMKDKSR 368 Query: 366 SGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAKT 415 +P+ M ++P T+GA+ DVV+ FWN ++ SV DA K A+A K+ Sbjct: 369 Q---LPNPE--MLLSPDTQGALIDVVTNFWNKNQ-SVDDAQKAFASALKS 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: 529 Number of extensions: 19 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