Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate GFF3852 PGA1_78p00160 putative sugar-binding periplasmic protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__Phaeo:GFF3852 Length = 409 Score = 211 bits (536), Expect = 4e-59 Identities = 146/423 (34%), Positives = 218/423 (51%), Gaps = 22/423 (5%) Query: 12 SLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVE-KDGFTWKDGAVAGGG 70 S+ +AL +S A+S +EV HWWTSGGE AAV V + W DGA+AG G Sbjct: 5 SILMTTALSVSATIAQS-ADLEVTHWWTSGGEAAAVTKFADAVNGQTTHNWVDGAIAGSG 63 Query: 71 GSTAMTVLKSRAVAGNPPGVAQIK-GPDIQEWGSTGLLSTDALKDVSKAENWDGLLSK-K 128 +TA ++ SR + G+P Q+ G +E GL++ L ++++ E W +++ Sbjct: 64 -TTARPIIISRILGGDPMAATQLTHGRQAEELIEAGLMTD--LTELAEQEGWRDIVNPPS 120 Query: 129 VSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGFIA 188 + D+ YEG VPVNIH WLW++ E F KAG+ P EF AA KL AG + Sbjct: 121 LLDSCTYEGRIYCVPVNIHSTQWLWLSHEAFDKAGMS-VPQDWYEFVAAAPKLAEAGIVP 179 Query: 189 LAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYMDP 248 LA G Q WQ F + + ++ D ++K ++ D +GP+ K F + + Sbjct: 180 LAMGQQGWQQRIAFGALTVGLVDQDSWRKVSLERDAGVAAGPQYAKVFDAVVDARE-LAR 238 Query: 249 NRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYNID 308 N +DWN+A VI+GKAG Q+MGDWA+ E+T A+++AG+DY C+ G + + D Sbjct: 239 NSNVQDWNLATNMVITGKAGGQIMGDWAQGEFTLAEQVAGQDYSCLPGMGLNQIIDTSGD 298 Query: 309 SMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDECA 368 A + D AQ D+A V + + Q F++ KGS+PVR D +D ++C Sbjct: 299 --AFYFPVIDDAEVRQAQMDMASVLISKEVQVDFNLTKGSLPVRGD----VDLSAANDCM 352 Query: 369 QKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLASAV 428 +K +AD G + PSM + A S Q I D++ F D A A A+ A + Sbjct: 353 KKGLA-ILAD---GNVLPSM--DQAFSADTQAQIQDLMAEFW-ASDMAAADAQARYAEII 405 Query: 429 KAA 431 A Sbjct: 406 ADA 408 Lambda K H 0.314 0.129 0.377 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: 458 Number of extensions: 22 Number of successful extensions: 7 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: 432 Length of database: 409 Length adjustment: 32 Effective length of query: 400 Effective length of database: 377 Effective search space: 150800 Effective search space used: 150800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 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