Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 5207560 Shew_0094 ABC transporter-related protein (RefSeq)
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__PV4:5207560 Length = 369 Score = 172 bits (436), Expect = 1e-47 Identities = 98/242 (40%), Positives = 142/242 (58%), Gaps = 4/242 (1%) Query: 11 KVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADP 70 K+F + + K GE + ++GPSG GK+T +RMIAGL +P G+I GD + Sbjct: 11 KIFQQEGIALDAEFVCKAGEVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFSS 70 Query: 71 EKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLGLT 130 E G ++ P+ R + V Q + L+P+MT N+ L +P+ E R ++ E + L Sbjct: 71 ESGRYLTPQQRHLGYVPQHFGLFPNMTALANVVAALD--HIPKAERVARAKDWLERVNLH 128 Query: 131 ELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLG 190 L +R P LSGGQRQRVAL RA+ R+P+V L+DEP S +D + R R+ EL +L+ QL Sbjct: 129 GLPDRLPANLSGGQRQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQLA 188 Query: 191 VTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSPPMNFLDA 250 + I VTHD EA+ + DR+ ++++G L Q GSP EV +P N VA +G N DA Sbjct: 189 IPVIMVTHDLNEALLLADRMILISQGTLLQQGSPREVLSRPRNEAVAKQMGL--RNLFDA 246 Query: 251 IV 252 V Sbjct: 247 HV 248 Lambda K H 0.323 0.142 0.406 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: 274 Number of extensions: 11 Number of successful extensions: 2 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: 372 Length of database: 369 Length adjustment: 30 Effective length of query: 342 Effective length of database: 339 Effective search space: 115938 Effective search space used: 115938 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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