Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_01454 H281DRAFT_01454 carbohydrate ABC transporter substrate-binding protein, CUT1 family
Query= reanno::WCS417:GFF4324 (428 letters) >FitnessBrowser__Burk376:H281DRAFT_01454 Length = 412 Score = 244 bits (622), Expect = 5e-69 Identities = 156/423 (36%), Positives = 215/423 (50%), Gaps = 21/423 (4%) Query: 7 LAVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAG 66 L ++ ++ + A+A K V +HWWTSGGE AA+ K G W D AVAG Sbjct: 8 LRAMVAALAMHGVLAYAEPLKANV--IHWWTSGGESAAIRQFADAYNKAGGQWIDNAVAG 65 Query: 67 GGGATAMTVLKSRAVAGNPPGVAQIK-GPDIQEWASTGLLDTDVLKDVAKEEKWDSLLDK 125 A + + +R V G+PP AQ + GLL+ + DVA +E W + + Sbjct: 66 ADQARSTAI--NRIVGGDPPTAAQFNTSKQFHDLIDQGLLNN--VDDVAAKENWSGVFPQ 121 Query: 126 KVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGFI 185 + D++K +G Y A PV+IH W + + F+KAGIT P + EF A KL+AAG I Sbjct: 122 SILDSIKVKGHYYAAPVDIHMPAWFFYSKPAFQKAGITAEPQSYDEFIADLGKLRAAGVI 181 Query: 186 PLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYMD 245 PLA GGQPWQ+ F+AV+ V G D Y K D D A+ K L K++ ++D Sbjct: 182 PLAFGGQPWQEKITFDAVLADVGGPDLYLKVYRDHDANAVKSDAFKKVLIAFKRLHDFVD 241 Query: 246 VDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYNI 305 G++WN VI+GKAG+QIMGDWAK E++AAK+ AGK++ C FPG Y + Sbjct: 242 AGSPGRNWNDATALVISGKAGVQIMGDWAKGEFSAAKQSAGKEFGC--FPGFGPHSPYLV 299 Query: 306 --DSLAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGFDSC 363 D K + T Q +A V+ Q FS KGSIP+R D +D+ D C Sbjct: 300 AGDVFVFPKSDNASTVKAQNLLATVMTSPPAQVAFSAKKGSIPIRPD----VDAGSLDIC 355 Query: 364 AQTAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKLGAA 423 A+ + D P M + T QGA DVVTN+ N ++ D K A Sbjct: 356 AKEGIA-IMKDKSRQLPNPEMLLSPDT----QGALIDVVTNFWNKNQS-VDDAQKAFAGA 409 Query: 424 IKS 426 +KS Sbjct: 410 LKS 412 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: 492 Number of extensions: 23 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: 428 Length of database: 412 Length adjustment: 32 Effective length of query: 396 Effective length of database: 380 Effective search space: 150480 Effective search space used: 150480 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