Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= SwissProt::P19566 (369 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 283 bits (725), Expect = 5e-81 Identities = 173/380 (45%), Positives = 229/380 (60%), Gaps = 41/380 (10%) Query: 14 GDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIGETRMNDIPPA 73 G+VVV INL+I DGEF+V VGPSGCGKSTLLR++AGLET + G + +G+ R++ +P Sbjct: 45 GEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAK 104 Query: 74 ERGVGMVFQSYALYPHLSVAENMSFGLKLAGAK------------------------KEV 109 R + MVFQSYALYPHLSV +N++FGL+ G + + Sbjct: 105 ARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEAR 164 Query: 110 MNQRVNQVAEVLQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALR 169 + +RV +VA +LQL LL+R+PK LSGGQ+QRVA+GR + P+VFL+DEPLSNLDA LR Sbjct: 165 IKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLR 224 Query: 170 VQMRIEISRLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRF 229 + R +I L ++LG T +YVTHDQ EAMT+ D+I VL+ G + QV PLE+Y PA+RF Sbjct: 225 AETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRF 284 Query: 230 VAGFIGSPKMNFLPVKVTA---TAIEQVQVELPNRQQIWLPVESRGVQVGANMSLGIRPE 286 VA FIGSP MN +PV V A E + LP + W PV + G + LGIRPE Sbjct: 285 VAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLP---EAWEPV--LRLYDGQTVELGIRPE 339 Query: 287 HLLPSDIADVTLEGEVQVVEQLGHETQIHIQIP----AIRQNLVYRQNDVVLVEEGATFA 342 HL A L V VE LG +T I ++ A++ L +Q + G Sbjct: 340 HLEVGAAASKNLLITVTGVEALGSDTFIAGELKESGIAVQARLAPQQ----CWQMGDRLW 395 Query: 343 IGLPPERCHLF-REDGSACR 361 + P++ HLF E G A R Sbjct: 396 LTFKPDQIHLFDLETGKAIR 415 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: 401 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: 369 Length of database: 417 Length adjustment: 31 Effective length of query: 338 Effective length of database: 386 Effective search space: 130468 Effective search space used: 130468 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