Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 196 bits (498), Expect = 8e-55 Identities = 115/283 (40%), Positives = 174/283 (61%), Gaps = 22/283 (7%) Query: 17 TAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGIFV 76 T +R + L + GE LLGPSGCGKTT L+ IAGL+ S+G+I I +L++ PE FV Sbjct: 17 TILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRISINGRLLSGPET--FV 74 Query: 77 PPKDRDIAMVFQSYALYPHMTVYDNIAFPLK-LRKVPRQEIDQRVREVAELLGLTELLNR 135 P + R++ M+FQ YAL+PH+TV +NI F +K L K RQ R+ E+ L+ L L R Sbjct: 75 PSERREVGMIFQDYALFPHLTVAENILFGVKGLDKAARQA---RLGEMLALVKLEGLGGR 131 Query: 136 KPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIY 195 P ELSGGQ+QRV++ RA+ +P++ L+DEP SN+DAK+R M E++++ +Q GV+ ++ Sbjct: 132 YPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVEIREILKQRGVSAVF 191 Query: 196 VTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSPPMNFLDAIVTED 255 VTH + EA D++A+ G + Q GS + +Y +P + +VA F+G +N+L V + Sbjct: 192 VTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFLGQ--VNYLSCEVKD- 248 Query: 256 GFVDFGEFRLKLLPDQFEVLGEL----GYVGREVIFGIRPEDL 294 RL+ L + + +L GY G + +RPE L Sbjct: 249 ------RARLQTLLGEVQSSSDLPKAAGYRGELL---LRPEQL 282 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: 317 Number of extensions: 18 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: 372 Length of database: 342 Length adjustment: 29 Effective length of query: 343 Effective length of database: 313 Effective search space: 107359 Effective search space used: 107359 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