Align ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized)
to candidate BPHYT_RS29190 BPHYT_RS29190 sugar ABC transporter substrate-binding protein
Query= reanno::Smeli:SMc04259 (411 letters) >FitnessBrowser__BFirm:BPHYT_RS29190 Length = 412 Score = 312 bits (799), Expect = 1e-89 Identities = 167/410 (40%), Positives = 242/410 (59%), Gaps = 12/410 (2%) Query: 3 LRFLAAALGATAALPFGAASATDLEVTHWWTSGGEAAAVAELAKAFDATGNKWVDGAIAG 62 LR + AAL + A V HWWTSGGE+AA+ + A A++ G +WVD A+AG Sbjct: 8 LRGVVAALALYGVV--AQAEPLKANVIHWWTSGGESAAIRQFADAYNKAGGQWVDNAVAG 65 Query: 63 SGGTARPIMISRITGGDPMAATQFNHGRQAEELVQAGLMRDLTDIATKENWKEIVKPSSL 122 + AR I+RI GGDP A QFN +Q +L+ GL+ ++ D+A KENW + P S+ Sbjct: 66 AD-QARSTAINRIVGGDPPTAAQFNTSKQFHDLIDQGLLNNVDDVAAKENWNGVF-PQSI 123 Query: 123 LDSCTIEGKIYCAPVNIHSWQWLWLSNAAFKQAGVE-VPKNWDEFVAAAPALEKAGIVPL 181 +DS ++G Y APV+IH W + S F++AG+ PK++DEF+A L+ AG++PL Sbjct: 124 IDSIKVKGHYYAAPVDIHMPAWFFYSKPVFQKAGIAGEPKSYDEFIADLGKLKTAGVIPL 183 Query: 182 AVGGQPWQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKV---FKAADDARRMS 238 A+GGQPWQ FD ++ + G + + KV+ +D KV FK D + Sbjct: 184 ALGGQPWQEKITFDAVLADVGGPDLYMKVYRDRDMNAVKSDAFKKVLASFKRLHDF--VD 241 Query: 239 KGTNVQDWNQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTGG 298 G+ ++WN AT +VI+GKAG QIMGDWA+GEF A Q AG D+ C PG G + G Sbjct: 242 PGSPGRNWNDATALVISGKAGVQIMGDWAKGEFSAANQSAGKDFGCFPGFGPHSPYLVAG 301 Query: 299 DAFYFPLLEDEEKSKAQEVLASTLLKPETQVAFNLKKGSLPVRGDVDLAAANDCMKKGLD 358 D F FP ++ KAQ +LA+ + P QVAF+ KKGS+P+R DVD ++ + C K+G+ Sbjct: 302 DVFVFPKTDNPTTIKAQNLLATVMTSPAAQVAFSAKKGSIPIRPDVDGSSLDICAKEGIA 361 Query: 359 ILA-KGNVIQGTDQLLSADSQKQKEDLFSEFFANHSMTPEDAQKRFADII 407 I+ K + + LLS D+Q D+ + F+ N + + +DAQK FA + Sbjct: 362 IMKDKSRQLPNPEMLLSPDTQGALIDVVTNFW-NKNQSVDDAQKAFASAL 410 Lambda K H 0.315 0.131 0.389 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: 479 Number of extensions: 19 Number of successful extensions: 5 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: 411 Length of database: 412 Length adjustment: 31 Effective length of query: 380 Effective length of database: 381 Effective search space: 144780 Effective search space used: 144780 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