Align glucose transporter, permease component (characterized)
to candidate WP_037456328.1 N825_RS20585 sugar ABC transporter permease
Query= reanno::Phaeo:GFF3640 (433 letters) >NCBI__GCF_000576635.1:WP_037456328.1 Length = 410 Score = 397 bits (1019), Expect = e-115 Identities = 209/415 (50%), Positives = 276/415 (66%), Gaps = 24/415 (5%) Query: 15 RGLFQQLELDVRLLGMIGAFVILCIGFNILTDGRFLTPRNIFNLTIQTVSVAIMATGMVF 74 R L LE+D RLL M A V++ +G +ILT G FLT RN++NL++QT V IMATGMV Sbjct: 17 RDLIAALEIDTRLLAMAAALVVIWVGLDILTGGIFLTARNLWNLSVQTSVVGIMATGMVL 76 Query: 75 VIVTRHIDLSVGALLATCSAVMAVVQTDVLPDMFGLGLNHPATWIITVAVGLAIGTLIGA 134 VIV RHIDLSVG+LL +MAV+Q ++LP + TW++++A GL G LIGA Sbjct: 77 VIVARHIDLSVGSLLGFVGMIMAVLQVEILP------IGTSWTWLVSLAAGLIAGCLIGA 130 Query: 135 FQGWMVGFLTIPAFIVTLGGFLVWRNVAWYLTDGQTIGPLDSTF-LVFGGTSGTLGTTLS 193 FQGW V + +PAFIVTLGG L++R +AW++T G+T+ P+D TF L+ GG G++G S Sbjct: 131 FQGWWVAYRAVPAFIVTLGGLLIFRGLAWWITQGRTVAPMDPTFQLMGGGLDGSIGAFWS 190 Query: 194 WVVGIVATLLALAALWNSRRAKQGHGFPVKPAWAEAVIAGSIAASILGFVAILNAYQIPA 253 WVVG V AL +R+ + FPV+P WAEA+I I+ FV ++N+Y P Sbjct: 191 WVVGAVFIAAALFKTVRTRQRRNRFNFPVRPLWAEALILAVSIGLIVSFVLVMNSYYRPR 250 Query: 254 RRLKRMMEAQGETMPEGLVVGYGLPISVLILIATAVVMTIIARRTRLGRYIFATGGNPDA 313 ++ + G+PI VLILI AV M+ + + T+ GRY+FA GGNP+A Sbjct: 251 TQIPQ-----------------GIPIPVLILIVVAVAMSALTKVTKFGRYVFAIGGNPEA 293 Query: 314 AELSGINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLDELRVIAAAVIGGTAL 373 AEL GIN R +TV IF LMGFL A+S + +ARL N G+L EL VIAAAVIGGT+L Sbjct: 294 AELGGINVRKVTVMIFVLMGFLAAISGAIQTARLNAGLNSTGSLLELSVIAAAVIGGTSL 353 Query: 374 SGGFGTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAAVWIDILYRKR 428 +GG GTI GAILGALIMQSLQSGM ++ + P Q +V+G VL+ AVW+D +Y+KR Sbjct: 354 AGGVGTIAGAILGALIMQSLQSGMILLDIATPMQPVVIGLVLIVAVWLDTVYQKR 408 Lambda K H 0.327 0.141 0.419 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: 651 Number of extensions: 40 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: 433 Length of database: 410 Length adjustment: 32 Effective length of query: 401 Effective length of database: 378 Effective search space: 151578 Effective search space used: 151578 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: 50 (23.9 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