Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate WP_090447189.1 BLS63_RS18140 carbohydrate ABC transporter substrate-binding protein
Query= reanno::WCS417:GFF4324 (428 letters) >NCBI__GCF_900100495.1:WP_090447189.1 Length = 417 Score = 528 bits (1360), Expect = e-154 Identities = 265/428 (61%), Positives = 317/428 (74%), Gaps = 11/428 (2%) Query: 1 MNAINRLAVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWK 60 MNAI+RLA A+S+ASL PLSA A G VEV+HWWTSGGEK AVD L+ VE G WK Sbjct: 1 MNAISRLATAVSLASLMPLSALA----GEVEVLHWWTSGGEKRAVDTLQKLVEDQGHSWK 56 Query: 61 DGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEKWD 120 D AVAGGGG AMTVLK+RAV+GNPP AQIKGPDIQEW GLL L VA+E++WD Sbjct: 57 DFAVAGGGGEAAMTVLKTRAVSGNPPAAAQIKGPDIQEWGELGLLAD--LDQVAEEQQWD 114 Query: 121 SLLDKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLK 180 LL ++V + +++ GDYVAVPVN+HRVNWLWINPEVF KAG T PTTL EF+AA DKLK Sbjct: 115 KLLPEQVVEVMQFGGDYVAVPVNVHRVNWLWINPEVFAKAGATP-PTTLDEFFAAADKLK 173 Query: 181 AAGFIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKV 240 AAGFIPLAHGGQPWQDSTVFE + L ++G + KA V+LD LTGP+MV+ L+K+ Sbjct: 174 AAGFIPLAHGGQPWQDSTVFEDLALGLLGPQDFHKAFVELDKDILTGPKMVEVFAALQKL 233 Query: 241 ATYMDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKA 300 Y+D + G+DWN V+NGKAGMQIMGDWAKSEWTAA KVAG DY+C+ FPGT + Sbjct: 234 HGYVDANAAGRDWNSATAMVMNGKAGMQIMGDWAKSEWTAAGKVAGSDYQCLPFPGTQGS 293 Query: 301 FTYNIDSLAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGF 360 F +NIDSLA+FK D Q+D+A+ V+G FQ+VF+ NKGSIPVR D D F Sbjct: 294 FAFNIDSLAMFKLSDADNRKAQEDLARTVMGTEFQRVFNQNKGSIPVRLD----QDMSVF 349 Query: 361 DSCAQTAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKL 420 D+CAQ + DF A A GGLQPS+AH MA + VQGA FDVVTN+ NDPKADP A++L Sbjct: 350 DACAQQSMADFKAAAANGGLQPSLAHGMAASSYVQGAVFDVVTNFFNDPKADPQKAAQQL 409 Query: 421 GAAIKSAK 428 AAI++ + Sbjct: 410 AAAIQAVQ 417 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: 585 Number of extensions: 27 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: 428 Length of database: 417 Length adjustment: 32 Effective length of query: 396 Effective length of database: 385 Effective search space: 152460 Effective search space used: 152460 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 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