Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__ANA3:7026373 Length = 349 Score = 121 bits (304), Expect = 2e-32 Identities = 72/207 (34%), Positives = 107/207 (51%), Gaps = 6/207 (2%) Query: 21 DLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTG----MPVQKRNVA 76 DL L +G + LLGP+ GKT+L+R +AGL + G I +G V+G +P ++R + Sbjct: 24 DLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQINGKTVSGAGQFVPSEQRGIG 83 Query: 77 MVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSGGQ 136 M++Q + +P LTV NI ++ A + L+KL R P LSGGQ Sbjct: 84 MIFQDYALFPHLTVAENIL--FGVAKLTPAQRKARLDDMLALVKLEGLAKRYPHELSGGQ 141 Query: 137 QQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSEAL 196 QQR ++ARAL L+L+DEP +N+D ++R + E+ I Q V+ T EA Sbjct: 142 QQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIRSILKQRNVSAVFVTHSKDEAF 201 Query: 197 LLGGNTATLNQGRVTQFGPTIEVYRRP 223 + A NQG + Q G +Y P Sbjct: 202 VFADTLAIFNQGVIVQHGRAENLYAAP 228 Lambda K H 0.319 0.136 0.392 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: 271 Number of extensions: 11 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: 358 Length of database: 349 Length adjustment: 29 Effective length of query: 329 Effective length of database: 320 Effective search space: 105280 Effective search space used: 105280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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