Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate WP_086510094.1 BZY95_RS11665 sugar ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_00020 (308 letters) >NCBI__GCF_002151265.1:WP_086510094.1 Length = 325 Score = 117 bits (294), Expect = 3e-31 Identities = 91/301 (30%), Positives = 148/301 (49%), Gaps = 22/301 (7%) Query: 19 RRLINPGWFLVSPSVALLLLWMIVPLAMTVYFSVIRYNLLNPGENEFVGLENFAYFVTDS 78 R+ + W ++P + L + PL T YFS +L + F+GLEN Y V D Sbjct: 27 RQRVRAAWLFLAPMLVTLAMVAGWPLLRTFYFSFTDASLSDMSNTLFIGLEN--YLVYDD 84 Query: 79 GFLPGAL----------NTLILVGSVLLISVIFGVLIAALLEASEFFGRGIVRVLLISPF 128 G G L NT+ + + V+FGV++A +L A EF GR +VR ++ P+ Sbjct: 85 GRWFGVLADPIWWRAVWNTVYFSVVSVSLEVVFGVIVALVLNA-EFKGRTLVRAAVLIPW 143 Query: 129 FIMPTVGSLIFKNLIFHPVSGILAAVWKFFG--AQPVDWLA--HYPLFSIIVIVSWQWLP 184 I PT+ S + + GI+ + G A P+ W A +Y ++++I++ W+ P Sbjct: 144 AI-PTIVSAQMWAWMLNDQFGIINHLLMALGIIASPIAWTADANYSMWAVIMVDVWKTTP 202 Query: 185 FAILLLMTAMQSLDQEQKEAARLDGAGALAIFWHLTLPHLARPIAVVVMIETIFLLSVFA 244 F LL++ A+Q L ++ EAA +DG + +F+ +TLP + + V V+ + L VF Sbjct: 203 FVALLVLAALQMLPKDCYEAAEVDGIHPVKVFFRVTLPLITPALMVAVIFRLLDALRVFD 262 Query: 245 EIFTTTNGGPGFASTNLAYLIYNQALVQF-DVGMASAGGLIAVVIANIAAIVLVRMIGKN 303 I+ T+ ST + Q LV+F DVG SA + +I +A I + + K Sbjct: 263 VIYVLTSNS---TSTMSMSIYARQQLVEFQDVGYGSAASTLLFLIIALATIAYLYLGRKQ 319 Query: 304 L 304 L Sbjct: 320 L 320 Lambda K H 0.329 0.142 0.429 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: 242 Number of extensions: 13 Number of successful extensions: 3 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: 308 Length of database: 325 Length adjustment: 27 Effective length of query: 281 Effective length of database: 298 Effective search space: 83738 Effective search space used: 83738 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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