Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate CCNA_01907 CCNA_01907 ABC transporter ATP-binding protein
Query= SwissProt::P19566 (369 letters) >FitnessBrowser__Caulo:CCNA_01907 Length = 253 Score = 146 bits (368), Expect = 7e-40 Identities = 84/220 (38%), Positives = 124/220 (56%), Gaps = 11/220 (5%) Query: 1 MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60 MA + RNV +GD VV +++ L I G FV VGPSG GKST LR++ G E T G + Sbjct: 1 MALLSFRNVWVEYGDKVVLENVELSIAQGSFVSIVGPSGAGKSTFLRLVIGQEAPTRGAI 60 Query: 61 FIGETRMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGL---------KLAGAKKEVMN 111 + + P +RGV VFQ Y+++PHLS +N+ FGL KL+GAK+ Sbjct: 61 DLEGRNLRAEPGPDRGV--VFQKYSVFPHLSARDNVVFGLDCAGSALRGKLSGAKRRAAL 118 Query: 112 QRVNQVAEVLQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQ 171 ++ + + + L + P +SGG +QR+AI + L+ +PR+ LLDEP LD +R+ Sbjct: 119 EQADAMLAAVGLGDSGDLYPAKMSGGMQQRLAIAQALIKKPRILLLDEPFGALDPGVRLD 178 Query: 172 MRIEISRLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGR 211 M I+ L + G T++ VTHD EA L +++ D R Sbjct: 179 MHELITSLWRDNGLTIMMVTHDIKEAFKLGTRVLAFDKRR 218 Lambda K H 0.321 0.138 0.396 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: 206 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: 369 Length of database: 253 Length adjustment: 27 Effective length of query: 342 Effective length of database: 226 Effective search space: 77292 Effective search space used: 77292 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: 48 (23.1 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