Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC
Query= reanno::Phaeo:GFF1302 (334 letters) >NCBI__GCF_000009985.1:WP_011385763.1 Length = 363 Score = 141 bits (355), Expect = 3e-38 Identities = 83/241 (34%), Positives = 128/241 (53%), Gaps = 32/241 (13%) Query: 22 LDLTIEDGEF------------TVFVGPSGCGKSTLLRLIAGLEDITSGTIRIDGE---- 65 LDL GEF T G SG GK++++ ++AGL G+I +DG Sbjct: 4 LDLRRRQGEFRLDVRLSAGPGVTALYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFD 63 Query: 66 --DATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALNL 123 ++PP R L VFQ + L+PH+SVR N+ F K+ +P+ E+ + +D L + Sbjct: 64 SRSGIDLPPEARRLGYVFQEHRLFPHLSVRGNLEFGQKL--LPSAERTQSLDKVVELLGI 121 Query: 124 TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRL 183 LDRRP +LSGG++QRVAIGRA++ P L DEPL+ LD A + + I++L +R Sbjct: 122 ESLLDRRPAKLSGGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRF 181 Query: 184 ATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMNLLT 243 + ++YV+H E + +AD + ++ G + G P+E +G P + LT Sbjct: 182 SVPILYVSHSMDEVLRLADTLALMDGGKVAASG-PLE-----------SLMGDPGLRPLT 229 Query: 244 G 244 G Sbjct: 230 G 230 Lambda K H 0.320 0.138 0.400 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: 306 Number of extensions: 19 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: 334 Length of database: 363 Length adjustment: 29 Effective length of query: 305 Effective length of database: 334 Effective search space: 101870 Effective search space used: 101870 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 (21.8 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