Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_000009985.1:WP_011385763.1 Length = 363 Score = 137 bits (346), Expect = 4e-37 Identities = 74/214 (34%), Positives = 123/214 (57%), Gaps = 11/214 (5%) Query: 23 DFNLDIQ---DKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVND------VP 73 +F LD++ T G SG GKT+ + M+AGL EG++ + R + D +P Sbjct: 12 EFRLDVRLSAGPGVTALYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFDSRSGIDLP 71 Query: 74 PKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKP 133 P+ R + VFQ + L+PH++V N+ FG KL +P AE + + + ++L I LLDR+P Sbjct: 72 PEARRLGYVFQEHRLFPHLSVRGNLEFGQKL--LPSAERTQSLDKVVELLGIESLLDRRP 129 Query: 134 KALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVT 193 LSGG++QRVA+GRA++ P++ LMDEPL+ LD + ++ I +L +R ++YV+ Sbjct: 130 AKLSGGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRFSVPILYVS 189 Query: 194 HDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQP 227 H E + + D + +M G + + + + P Sbjct: 190 HSMDEVLRLADTLALMDGGKVAASGPLESLMGDP 223 Lambda K H 0.321 0.138 0.395 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: 317 Number of extensions: 12 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: 384 Length of database: 363 Length adjustment: 30 Effective length of query: 354 Effective length of database: 333 Effective search space: 117882 Effective search space used: 117882 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: 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