Align Sugar ABC transporter, periplasmic sugar-binding protein (characterized, see rationale)
to candidate SMc03813 SMc03813 periplasmic binding ABC transporter protein
Query= uniprot:Q9WXW9 (335 letters) >FitnessBrowser__Smeli:SMc03813 Length = 337 Score = 114 bits (284), Expect = 5e-30 Identities = 106/342 (30%), Positives = 151/342 (44%), Gaps = 54/342 (15%) Query: 13 MRKLLVFLSVL-LVAGLS----------LALTIGVIGKSVHPYWSQVEQGVKAAGKALG- 60 +R L LSV L AGL+ AL V+ + P ++QG +AA K LG Sbjct: 4 VRTLTAALSVACLAAGLTAPQANAADREFALVFKVLNNAFSP---PIQQGCEAAAKKLGD 60 Query: 61 VDTKFFVPQKEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDT 120 V + P + D Q+Q+ + + GV G+ ++ +P A+ +K A + GIPVVT DT Sbjct: 61 VTCTYLGPTEYDEAKQVQLAQDMVTRGVAGLGVSAGNPKAMARIMKMAQDKGIPVVTFDT 120 Query: 121 D--SPDSG-RYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKD 177 D D+G R YIGTDNY+ G + E G V I +G+ + N R+QG +D Sbjct: 121 DVLPEDAGLRSTYIGTDNYEFGIALAQKVLESKKDGGTVCIQSGAPASENLKARVQGIRD 180 Query: 178 AI----KDSEIEIVDILN-----------DEEDGARAVSLAEAALNAHPDLDAFFGV--- 219 + KD E + N + +D A + +P+L AF V Sbjct: 181 TLAGVTKDKGAEKLTGQNGWTEPAGCPVYNNDDITLAAQQVRDVMTNNPELSAFVAVGGW 240 Query: 220 --YAYNGPAQALVVKNAGKVGKVKIVCF-DTTPDILQYVKEGVIQATMGQRPYMMGYLSV 276 YA QA+ A K +V F D L + EG+ +GQRPY MGY Sbjct: 241 AQYAPQAYKQAMEPLKARLDSKDLVVVFGDNFGPQLPLLAEGLSHYNIGQRPYDMGY--- 297 Query: 277 TVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPEN 318 T+M L K+ KV+ I TG +V TPE+ Sbjct: 298 ------------ETIMALDKLTKGEKVEPFIKTGTEVCTPED 327 Lambda K H 0.318 0.137 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: 228 Number of extensions: 11 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: 335 Length of database: 337 Length adjustment: 28 Effective length of query: 307 Effective length of database: 309 Effective search space: 94863 Effective search space used: 94863 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 (21.7 bits) S2: 49 (23.5 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