Align LacI family transcriptional regulator; SubName: Full=Ribose transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_004110580.1 RHSP_RS05955 sugar ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UEH6 (318 letters) >NCBI__GCF_000359745.1:WP_004110580.1 Length = 328 Score = 261 bits (667), Expect = 2e-74 Identities = 140/318 (44%), Positives = 208/318 (65%), Gaps = 12/318 (3%) Query: 1 MKLPFAGRLLAVAVLAAASAALPLSSAFADDAAKPKVGLVMKSLANEFFVTMQDGAKTYQ 60 +KL AG L VLA + P AFA A KPKVGL+MKSL+NEFF M+ GA Y Sbjct: 20 LKLGLAGTL----VLALSCGVSP---AFA--AGKPKVGLIMKSLSNEFFKQMKAGADKYA 70 Query: 61 KEHAADFDMITNGIKNETDTSAQIDIVNQMILAKVNAIVIAPADSKALVTVLKKASDAGI 120 E+ FD G+K+E D +AQ+D V + K + IV+APADSKA+ T L KA AG+ Sbjct: 71 AENKDKFDFKAVGMKDERDFAAQVDAVENFVTQKYDIIVVAPADSKAMATPLAKAVKAGV 130 Query: 121 KVVNIDNRLDPDVLKSKNLDIPFVGPDNRKGSKLVGDYLAKQLASGDKVGIIEGVPTTTN 180 KV+NID LD D K+ +D+ F GPDN++G+KL GD LAK L G KV I+EG P N Sbjct: 131 KVINIDVPLDADAKKAAGIDLAFFGPDNKEGAKLAGDALAKDLGPGAKVVILEGNPEADN 190 Query: 181 AQQRTAGYKDAMDAAGMKIVSTQSGNWEIDQGQKVASAMLSEYPDLKALLAGNDNMALGA 240 A++R G+ D++ ++++ +++ +WE ++ V + L++Y +++ ++A ND+MALG Sbjct: 191 AKERKEGFVDSIKGGKLELLDSKTAHWETEEANTVMTNFLTKYKNIQGVMAANDSMALGV 250 Query: 241 VSAVRAAGKAGKVLVVGYDNIEAIKPMLQDGRVLATADQAAAQQAVFGIQNALKLVKGEK 300 V A+ A+G++GK+ VVG+DNI +KP+++DG++LAT +Q A+ AV GI+ L+ + GEK Sbjct: 251 VKALDASGQSGKIKVVGFDNIPPVKPLIKDGKMLATVEQYGAEMAVMGIKYGLRELGGEK 310 Query: 301 VDSKDGVIETPVELVLKK 318 G ++T ++LV K Sbjct: 311 F---SGWVKTDIKLVTTK 325 Lambda K H 0.314 0.130 0.349 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: 300 Number of extensions: 13 Number of successful extensions: 1 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: 318 Length of database: 328 Length adjustment: 28 Effective length of query: 290 Effective length of database: 300 Effective search space: 87000 Effective search space used: 87000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 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