Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate SMc04396 SMc04396 periplasmic binding protein
Query= reanno::WCS417:GFF4324 (428 letters) >FitnessBrowser__Smeli:SMc04396 Length = 414 Score = 352 bits (904), Expect = e-102 Identities = 192/426 (45%), Positives = 259/426 (60%), Gaps = 13/426 (3%) Query: 4 INRLAVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGA 63 + + ++A+L L+A AA + VEV+HWWTSGGE AA+DVLK +E G W D Sbjct: 1 MRKFMTTTAVAALM-LAATAARAAENVEVLHWWTSGGEAAALDVLKKDLESKGISWTDMP 59 Query: 64 VAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEKWDSLL 123 VAGGGG AMTVL++R AGN P Q+ G DI +WA G L L +VA +E WD ++ Sbjct: 60 VAGGGGTEAMTVLRARVTAGNAPTAVQMLGFDILDWAKEGALGN--LDEVAAKEGWDKVV 117 Query: 124 DKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAG 183 + KY+G ++A PVN+H NW+WIN KAG K PTT +E A DK K G Sbjct: 118 PAALQQFSKYDGHWIAAPVNVHSTNWVWINKAALDKAG-AKEPTTWEELIALLDKFKEQG 176 Query: 184 FIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATY 243 P+AHGGQPWQD+T+F+AVVLS +G D YK+A +DLD AL G +M +A + K+ +Y Sbjct: 177 ITPIAHGGQPWQDATIFDAVVLS-LGNDFYKQAFIDLDPAALGGDKMKEAFDRMTKLRSY 235 Query: 244 MDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTY 303 +D + G+DWNL + VI KAG+Q MGDWAK E+ AKKV G D+ C+ FPGT + T+ Sbjct: 236 VDDNFSGRDWNLASAMVIENKAGLQFMGDWAKGEFLKAKKVPGTDFVCMRFPGTQGSVTF 295 Query: 304 NIDSLAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGFDSC 363 N D A+FK + A Q +A + FQ F++ KGS+P R D + FD+C Sbjct: 296 NSDQFAMFKVSEDKVPA-QLQMASAIESPAFQSAFNVVKGSVPARTD----VPDTDFDAC 350 Query: 364 AQTAAKDFLADAKTGG-LQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKLGA 422 + KD LA+A T G L SMAH A AV+ A +DVVT N + + + +L A Sbjct: 351 GKKGIKD-LAEANTNGTLFGSMAHGHANPAAVKNAIYDVVTRQFNG-ELNSEEAVTELVA 408 Query: 423 AIKSAK 428 A+++AK Sbjct: 409 AVEAAK 414 Lambda K H 0.314 0.131 0.388 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: 500 Number of extensions: 24 Number of successful extensions: 6 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: 428 Length of database: 414 Length adjustment: 32 Effective length of query: 396 Effective length of database: 382 Effective search space: 151272 Effective search space used: 151272 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: 42 (22.0 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