Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 2 (characterized)
to candidate HSERO_RS02195 HSERO_RS02195 sugar ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3041 (299 letters) >FitnessBrowser__HerbieS:HSERO_RS02195 Length = 324 Score = 370 bits (950), Expect = e-107 Identities = 181/290 (62%), Positives = 226/290 (77%), Gaps = 2/290 (0%) Query: 6 PQRKSRVANPGWFLVSPSVALLLLWMIVPLGMTVYFSTIRYNLLNPGENEFVGLENFTYF 65 P RK R NP + +PSV +LL WMIVPL MT+YFS RYNL+ P + FVGLEN+ + Sbjct: 31 PPRKERF-NPIRLMQTPSVLILLAWMIVPLAMTIYFSVNRYNLMAPDQTGFVGLENYAFL 89 Query: 66 LTDSGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFFGRGIVRVMLISPFFIMPTV 125 L D F P NT LL+GSVL ISV+ G L++ L + F GRGI R+++I PFF+MPTV Sbjct: 90 LQDPAFWPSIGNTALLIGSVLAISVIGGTLLAVLFD-QPFRGRGIARLLVIGPFFVMPTV 148 Query: 126 GALIWKNLIFHPVSGILAYVWKLFGAQPVDWLAHYPLLSIIIIVSWQWLPFAILILMTAM 185 ALIWKN+I HPV GILAYV + G +P+DWLA YP+LS+IIIV+WQW+PFA LIL+TA+ Sbjct: 149 AALIWKNMIMHPVYGILAYVMRHLGLEPIDWLAEYPMLSVIIIVAWQWIPFAFLILLTAL 208 Query: 186 QSLDQEQKEAARLDGAGPIAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGP 245 QSLD +QKEAA+LDGAGP+ IF+++ LPHL R I VV+MIETIFLLSVFAEIFTTT GGP Sbjct: 209 QSLDTDQKEAAQLDGAGPVRIFFYIVLPHLKRAITVVIMIETIFLLSVFAEIFTTTAGGP 268 Query: 246 GYASTNLAYLIYNQALVQFDVGMASAGGLIAVVIANIAAIILVRMIGKNL 295 G A+TNL +L+Y+ L QFD+G+ASAGG+ AVV+ANI + LVRM+ +NL Sbjct: 269 GTATTNLTFLVYSIGLQQFDIGIASAGGIFAVVLANIVSFFLVRMLARNL 318 Lambda K H 0.328 0.142 0.436 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: 319 Number of extensions: 10 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: 299 Length of database: 324 Length adjustment: 27 Effective length of query: 272 Effective length of database: 297 Effective search space: 80784 Effective search space used: 80784 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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