Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC
Query= BRENDA::P68187 (371 letters) >NCBI__GCF_000009985.1:WP_011385763.1 Length = 363 Score = 147 bits (371), Expect = 4e-40 Identities = 101/324 (31%), Positives = 166/324 (51%), Gaps = 24/324 (7%) Query: 21 DINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIGEKRMNDT------PPAE 74 D+ L G ++ G SG GK++++ M+AGL G + + + + D+ PP Sbjct: 16 DVRLSAGPGVTALY-GRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFDSRSGIDLPPEA 74 Query: 75 RGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEVLQLAHLLDRKPKAL 134 R +G VFQ + L+PHLSV N+ FG KL + + Q +++V E+L + LLDR+P L Sbjct: 75 RRLGYVFQEHRLFPHLSVRGNLEFGQKLLPSAERT--QSLDKVVELLGIESLLDRRPAKL 132 Query: 135 SGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHDQ 194 SGG++QRVAIGR L+A P + L+DEPL+ LD A + ++ I++L +R ++YV+H Sbjct: 133 SGGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRFSVPILYVSHSM 192 Query: 195 VEAMTLADKIVVLDAGRVAQVGKPLELY-----------HYPADRFVAGFIGSPKMNFLP 243 E + LAD + ++D G+VA G PLE Y A + + S F Sbjct: 193 DEVLRLADTLALMDGGKVAASG-PLESLMGDPGLRPLTGRYEAGAVIGAVVSSHDSGFGI 251 Query: 244 VKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADVILEGE 303 ++ + +P +V L + +RDV + + ++LP+ + V Sbjct: 252 SRLAFDGGTLIVGRSELPVGAKVRLRIHARDVAIAIEPPDRVSIRNVLPAIVVSVAPADS 311 Query: 304 --VQVVEQLGNETQIHIQIPSIRQ 325 V V+ G T+ +QI ++ Q Sbjct: 312 FLVDVILACG-PTRFWVQITTLAQ 334 Lambda K H 0.320 0.137 0.393 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: 343 Number of extensions: 13 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: 371 Length of database: 363 Length adjustment: 30 Effective length of query: 341 Effective length of database: 333 Effective search space: 113553 Effective search space used: 113553 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