Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate SMc04259 SMc04259 periplasmic binding ABC transporter signal peptide protein
Query= reanno::WCS417:GFF4324 (428 letters) >FitnessBrowser__Smeli:SMc04259 Length = 411 Score = 218 bits (554), Expect = 4e-61 Identities = 127/347 (36%), Positives = 179/347 (51%), Gaps = 10/347 (2%) Query: 7 LAVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAG 66 LA A+ + P F A S +EV HWWTSGGE AAV L + G W DGA+AG Sbjct: 6 LAAALGATAALP---FGAASATDLEVTHWWTSGGEAAAVAELAKAFDATGNKWVDGAIAG 62 Query: 67 GGGATAMTVLKSRAVAGNPPGVAQIK-GPDIQEWASTGLLDTDVLKDVAKEEKWDSLLD- 124 GG TA ++ SR G+P Q G +E GL+ L D+A +E W ++ Sbjct: 63 SGG-TARPIMISRITGGDPMAATQFNHGRQAEELVQAGLMRD--LTDIATKENWKEIVKP 119 Query: 125 KKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGF 184 + D+ EG PVNIH WLW++ FK+AG+ + P EF AA L+ AG Sbjct: 120 SSLLDSCTIEGKIYCAPVNIHSWQWLWLSNAAFKQAGV-EVPKNWDEFVAAAPALEKAGI 178 Query: 185 IPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYM 244 +PLA GGQPWQ + F+ +++++ G + ++K D GPE+ K A M Sbjct: 179 VPLAVGGQPWQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADD-ARRM 237 Query: 245 DVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYN 304 QDWN VI GKAG QIMGDWA+ E+ A + AG DY C+ G ++ + Sbjct: 238 SKGTNVQDWNQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTG 297 Query: 305 IDSLAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDM 351 D+ +D+ + Q+ +A +L Q F++ KGS+PVR D+ Sbjct: 298 GDAFYFPLLEDEEKSKAQEVLASTLLKPETQVAFNLKKGSLPVRGDV 344 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: 520 Number of extensions: 27 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: 411 Length adjustment: 32 Effective length of query: 396 Effective length of database: 379 Effective search space: 150084 Effective search space used: 150084 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