Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate WP_011653613.1 RL_RS21735 carbohydrate ABC transporter permease
Query= reanno::Phaeo:GFF1303 (276 letters) >NCBI__GCF_000009265.1:WP_011653613.1 Length = 276 Score = 444 bits (1142), Expect = e-129 Identities = 218/276 (78%), Positives = 246/276 (89%) Query: 1 MARAVTPRRKAINTALAWAVGLLIFFPILWTILTSFKTEAQAISDPPVFLFFDWTLENYS 60 MAR VT +RK I TA+AW +G+LIFFPILWT LTSFK+EA AI+ PP FLFF WT ENY+ Sbjct: 1 MARKVTTKRKLIVTAIAWTLGILIFFPILWTFLTSFKSEADAIASPPQFLFFHWTTENYA 60 Query: 61 VVQERSDYMRFLWNSVIIAGGSTILGIIIAVPAAWSMAFVPSKRTKDILLWMLSTKMLPA 120 VQ RS+Y+ NSV+I+ GST++G+IIA+PAAW+MAF P+KRTKD+L+WMLSTKM+P Sbjct: 61 EVQSRSNYLGHFMNSVVISFGSTLIGLIIAIPAAWAMAFSPTKRTKDVLMWMLSTKMMPP 120 Query: 121 VGVLYPIYILFIKMGLLDNRFGLVVVLMLINLPIIVWMLYTYFKEIPGEILEAARMDGAT 180 VG L PIY++F GLLD R GLV+VL LINLPIIVWMLYTYFKEIPGEILEAARMDGA+ Sbjct: 121 VGALIPIYLMFRNFGLLDTRTGLVIVLTLINLPIIVWMLYTYFKEIPGEILEAARMDGAS 180 Query: 181 LKEEILYVLTPMAIPGIASTLLLNIILAWNEAFWTLNLTAAKAAPLTAFIASYSSPEGLF 240 L +EI+YVLTPMA+PGIASTLLLNIILAWNEAFWTLNLTA+KAAPLTAFIASYSSPEGLF Sbjct: 181 LMKEIVYVLTPMAVPGIASTLLLNIILAWNEAFWTLNLTASKAAPLTAFIASYSSPEGLF 240 Query: 241 YAKLSAASTMAIAPILILGWFSQKQLVSGLTFGAVK 276 YAKLSAASTMAIAPILILGWFSQKQLV GLTFGAVK Sbjct: 241 YAKLSAASTMAIAPILILGWFSQKQLVRGLTFGAVK 276 Lambda K H 0.327 0.139 0.428 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: 430 Number of extensions: 15 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: 276 Length of database: 276 Length adjustment: 25 Effective length of query: 251 Effective length of database: 251 Effective search space: 63001 Effective search space used: 63001 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 47 (22.7 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