Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_000009985.1:WP_011385763.1 Length = 363 Score = 136 bits (343), Expect = 8e-37 Identities = 97/290 (33%), Positives = 149/290 (51%), Gaps = 28/290 (9%) Query: 36 LVGPSGCGKSTLMNCIAGLETISGGAILVDDADI----SGMS--PKDRDIAMVFQSYALY 89 L G SG GK++++N +AGL G+I VD + SG+ P+ R + VFQ + L+ Sbjct: 28 LYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFDSRSGIDLPPEARRLGYVFQEHRLF 87 Query: 90 PTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRA 149 P +SVR N+ FG K+ +P+AE + + +V +LL IE LL R+P +LSGG++QRVA+GRA Sbjct: 88 PHLSVRGNLEFGQKL--LPSAERTQSLDKVVELLGIESLLDRRPAKLSGGEKQRVAIGRA 145 Query: 150 LARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVM 209 L P+I L DEPL+ LD + E+ + + +R +YV+H E + L D +A+M Sbjct: 146 LLASPRILLMDEPLAALDPARKAEVLPFIAQLARRFSVPILYVSHSMDEVLRLADTLALM 205 Query: 210 KDGIIQQFGTPKDIYNNP----------ANLFVASFIGSPPMNFIPLRLQRKDGRLLALL 259 G + G + + +P A + + + S F RL G L+ Sbjct: 206 DGGKVAASGPLESLMGDPGLRPLTGRYEAGAVIGAVVSSHDSGFGISRLAFDGGTLIV-- 263 Query: 260 DSGQARCELPLGMQ-DAGLEDREVILGIRPEQIILANGEANGLPTIRAEV 308 R ELP+G + + R+V + I P + N LP I V Sbjct: 264 ----GRSELPVGAKVRLRIHARDVAIAIEPPDRVSIR---NVLPAIVVSV 306 Lambda K H 0.319 0.138 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: 357 Number of extensions: 16 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: 386 Length of database: 363 Length adjustment: 30 Effective length of query: 356 Effective length of database: 333 Effective search space: 118548 Effective search space used: 118548 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: 50 (23.9 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