Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate PP_5137 PP_5137 ferric iron ABC transporter, ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Putida:PP_5137 Length = 352 Score = 237 bits (605), Expect = 3e-67 Identities = 140/340 (41%), Positives = 205/340 (60%), Gaps = 14/340 (4%) Query: 2 AGVRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIY 61 A +++ ++ K FG TA+ ++SL++ GE + LLGPSGCGKTT LR IAGLE RG +Y Sbjct: 8 AQIKVRNIHKRFGAFTALNDVSLDIAAGELVCLLGPSGCGKTTLLRCIAGLERQDRGTLY 67 Query: 62 IGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVR 121 IG++ ++D + P+ RD ++FQSYAL+P++TV NIA+ L R++ QRV Sbjct: 68 IGERDISD------LSPQARDYGILFQSYALFPNLTVEANIAYGLT--GSGREQARQRVA 119 Query: 122 EVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAE 181 E+ EL+GL+ + P +LSGGQ+QRVAL RA+ P + L+DEP+S LDA++R + E Sbjct: 120 EMLELVGLSGSEKKYPGQLSGGQQQRVALARALAPSPSLLLLDEPMSALDARVREHLCTE 179 Query: 182 LKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIG 241 L++LQRQLG+TT+ VTH+Q EAM M DRIAVMN G ++Q +P E+YD PA FVA F+G Sbjct: 180 LRQLQRQLGITTLMVTHNQDEAMLMADRIAVMNNGQVEQYATPQEIYDHPATPFVAEFVG 239 Query: 242 SPPMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGREVIF---GIRPEDLYDAM 298 N+L + D G+ ++L P + + E I + E+L+ AM Sbjct: 240 QG--NWLPFQRSSDSHALVGDMNMRLAPGSAQASSGRLFCRPEAITVNPVVHEENLFPAM 297 Query: 299 FAQVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGS 338 ++ G N R E+ G + L + +GS Sbjct: 298 VREITFLG-NRCRMSFELKALPGHALLAELAPEAMPRLGS 336 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: 345 Number of extensions: 17 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: 352 Length adjustment: 29 Effective length of query: 343 Effective length of database: 323 Effective search space: 110789 Effective search space used: 110789 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