Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate Ac3H11_2062 ABC-type sugar transport system, periplasmic component
Query= reanno::WCS417:GFF4324 (428 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2062 Length = 416 Score = 430 bits (1105), Expect = e-125 Identities = 222/419 (52%), Positives = 277/419 (66%), Gaps = 12/419 (2%) Query: 8 AVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAGG 67 AVA+ +A+ SA G VEV+H+WTSGGE +V LK ++ G W+D AVAGG Sbjct: 9 AVAVGLAAAMSASA------GEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGG 62 Query: 68 GGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEKWDSLLDKKV 127 GG +AMTVLKSR ++GNPP AQ KGP IQEWAS G+L + +AK EKWD LL K V Sbjct: 63 GGDSAMTVLKSRVISGNPPSAAQTKGPAIQEWASEGVLAN--MDTLAKAEKWDELLPKVV 120 Query: 128 SDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGFIPL 187 +D +KY+G YVA PVN+HRVNW+W + E KKAG+ P T EF+AA DKLKAAG +P+ Sbjct: 121 ADVMKYKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPV 180 Query: 188 AHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYMDVD 247 AHGGQ WQD T FE+VVL V GA Y+ ALV LDN ALT M K+L +++ Y D Sbjct: 181 AHGGQNWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPG 240 Query: 248 GKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYNIDS 307 G+DWNL +I GKAG Q+MGDWAK E+ AA K GKD+ C A PG+ AFT+N+DS Sbjct: 241 APGRDWNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDS 300 Query: 308 LAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGFDSCAQTA 367 +FK KD Q D+A ++ FQ+VF++NKGSIPVR MD FD CA+ + Sbjct: 301 FILFKLKDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAG--QPMDK--FDDCAKAS 356 Query: 368 AKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKLGAAIKS 426 AKDF+ AK+GGL PS AH MA A +GA DVV+ + ND K AD KK+ AA K+ Sbjct: 357 AKDFVDTAKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAKT 415 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: 583 Number of extensions: 24 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: 416 Length adjustment: 32 Effective length of query: 396 Effective length of database: 384 Effective search space: 152064 Effective search space used: 152064 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