Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate GFF3852 PGA1_78p00160 putative sugar-binding periplasmic protein
Query= reanno::WCS417:GFF4324 (428 letters) >FitnessBrowser__Phaeo:GFF3852 Length = 409 Score = 219 bits (559), Expect = 9e-62 Identities = 142/384 (36%), Positives = 205/384 (53%), Gaps = 29/384 (7%) Query: 10 AISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAV----DVLKAQVEKDGFVWKDGAVA 65 +I + + +SA A S +EV HWWTSGGE AAV D + Q + W DGA+A Sbjct: 5 SILMTTALSVSATIAQS-ADLEVTHWWTSGGEAAAVTKFADAVNGQTTHN---WVDGAIA 60 Query: 66 GGGGATAMTVLKSRAVAGNPPGVAQIK-GPDIQEWASTGLLDTDVLKDVAKEEKWDSLLD 124 G G TA ++ SR + G+P Q+ G +E GL+ TD L ++A++E W +++ Sbjct: 61 GSG-TTARPIIISRILGGDPMAATQLTHGRQAEELIEAGLM-TD-LTELAEQEGWRDIVN 117 Query: 125 K-KVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAG 183 + D+ YEG VPVNIH WLW++ E F KAG++ P EF AA KL AG Sbjct: 118 PPSLLDSCTYEGRIYCVPVNIHSTQWLWLSHEAFDKAGMSV-PQDWYEFVAAAPKLAEAG 176 Query: 184 FIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVK---ALTELKKV 240 +PLA G Q WQ F A+ + ++ D ++K ++ D G GP+ K A+ + +++ Sbjct: 177 IVPLAMGQQGWQQRIAFGALTVGLVDQDSWRKVSLERDAGVAAGPQYAKVFDAVVDAREL 236 Query: 241 ATYMDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKA 300 A +V QDWNL VI GKAG QIMGDWA+ E+T A++VAG+DY C+ G ++ Sbjct: 237 ARNSNV----QDWNLATNMVITGKAGGQIMGDWAQGEFTLAEQVAGQDYSCLPGMGLNQI 292 Query: 301 FTYNIDSLAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGF 360 + D+ D Q D+A V++ + Q F++ KGS+PVR D+ Sbjct: 293 IDTSGDAFYFPVIDDAEVRQAQMDMASVLISKEVQVDFNLTKGSLPVRGDV--------D 344 Query: 361 DSCAQTAAKDFLADAKTGGLQPSM 384 S A K LA G + PSM Sbjct: 345 LSAANDCMKKGLAILADGNVLPSM 368 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: 498 Number of extensions: 29 Number of successful extensions: 4 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: 409 Length adjustment: 32 Effective length of query: 396 Effective length of database: 377 Effective search space: 149292 Effective search space used: 149292 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