Align ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized)
to candidate GFF3852 PGA1_78p00160 putative sugar-binding periplasmic protein
Query= reanno::Smeli:SMc04259 (411 letters) >FitnessBrowser__Phaeo:GFF3852 Length = 409 Score = 514 bits (1324), Expect = e-150 Identities = 259/402 (64%), Positives = 311/402 (77%), Gaps = 4/402 (0%) Query: 13 TAALPFGA--ASATDLEVTHWWTSGGEAAAVAELAKAFDA-TGNKWVDGAIAGSGGTARP 69 T AL A A + DLEVTHWWTSGGEAAAV + A A + T + WVDGAIAGSG TARP Sbjct: 9 TTALSVSATIAQSADLEVTHWWTSGGEAAAVTKFADAVNGQTTHNWVDGAIAGSGTTARP 68 Query: 70 IMISRITGGDPMAATQFNHGRQAEELVQAGLMRDLTDIATKENWKEIVKPSSLLDSCTIE 129 I+ISRI GGDPMAATQ HGRQAEEL++AGLM DLT++A +E W++IV P SLLDSCT E Sbjct: 69 IIISRILGGDPMAATQLTHGRQAEELIEAGLMTDLTELAEQEGWRDIVNPPSLLDSCTYE 128 Query: 130 GKIYCAPVNIHSWQWLWLSNAAFKQAGVEVPKNWDEFVAAAPALEKAGIVPLAVGGQPWQ 189 G+IYC PVNIHS QWLWLS+ AF +AG+ VP++W EFVAAAP L +AGIVPLA+G Q WQ Sbjct: 129 GRIYCVPVNIHSTQWLWLSHEAFDKAGMSVPQDWYEFVAAAPKLAEAGIVPLAMGQQGWQ 188 Query: 190 ANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADDARRMSKGTNVQDWNQA 249 AF L V + ++++ KV ++D VAAGP+ AKVF A DAR +++ +NVQDWN A Sbjct: 189 QRIAFGALTVGLVDQDSWRKVSLERDAGVAAGPQYAKVFDAVVDARELARNSNVQDWNLA 248 Query: 250 TNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTGGDAFYFPLLEDE 309 TNMVITGKAGGQIMGDWAQGEF LA Q AG DY+CLPG+G+N++I T GDAFYFP+++D Sbjct: 249 TNMVITGKAGGQIMGDWAQGEFTLAEQVAGQDYSCLPGMGLNQIIDTSGDAFYFPVIDDA 308 Query: 310 EKSKAQEVLASTLLKPETQVAFNLKKGSLPVRGDVDLAAANDCMKKGLDILAKGNVIQGT 369 E +AQ +AS L+ E QV FNL KGSLPVRGDVDL+AANDCMKKGL ILA GNV+ Sbjct: 309 EVRQAQMDMASVLISKEVQVDFNLTKGSLPVRGDVDLSAANDCMKKGLAILADGNVLPSM 368 Query: 370 DQLLSADSQKQKEDLFSEFFANHSMTPEDAQKRFADIIAAAD 411 DQ SAD+Q Q +DL +EF+A+ M DAQ R+A+IIA AD Sbjct: 369 DQAFSADTQAQIQDLMAEFWAS-DMAAADAQARYAEIIADAD 409 Lambda K H 0.315 0.131 0.389 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: 551 Number of extensions: 22 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: 411 Length of database: 409 Length adjustment: 31 Effective length of query: 380 Effective length of database: 378 Effective search space: 143640 Effective search space used: 143640 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: 41 (21.6 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