Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 290 bits (741), Expect = 6e-83 Identities = 173/400 (43%), Positives = 241/400 (60%), Gaps = 42/400 (10%) Query: 3 MAQVVLENVTKVY--------ENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAG 54 +A VV E + K + + +VV + NL + D EF+V++GPSGCGK+T LR++AG Sbjct: 23 VAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAG 82 Query: 55 LEEITDGKIYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLK---------- 104 LE + G I + + V+ + K RDIAMVFQ+YALYPH++VY+N+AFGL+ Sbjct: 83 LETPSRGLIKVGDRRVDRLPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQ 142 Query: 105 -----LRKYPKD---------EIDRRVREAAKILGIENLLDRKPRQLSGGQRQRVAVGRA 150 R PK I RRVRE A +L ++ LLDR+P+QLSGGQ+QRVA+GRA Sbjct: 143 QLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRA 202 Query: 151 IVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQATIIYVTHDQVEAMTMADKIVVM 210 I RNP+VFL DEPLSNLDAKLR + R+++ L +L T +YVTHDQ EAMTM D+I V+ Sbjct: 203 IARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVL 262 Query: 211 KDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNARVVRGEGGLWIQASGFKVKVPKE 270 G +QQ+ +P EIY+ PAN FVA FIGSPPMN + V L + F+ +P+ Sbjct: 263 NRGHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIPVTV---RAPLQLTTENFRCTLPEA 319 Query: 271 FEDKLANYIDKEIIFGIRPEDIYDKLFALAPSPENTITGVVDVVEPLGSETIL--HVKVG 328 +E L Y + + GIRPE + + A + + T+TG VE LGS+T + +K Sbjct: 320 WEPVLRLYDGQTVELGIRPEHL-EVGAAASKNLLITVTG----VEALGSDTFIAGELKES 374 Query: 329 DDLIVASVNPRTQAKEEQKIDLVLDMTRMHAFDKETEKAI 368 + A + P+ + ++ L ++H FD ET KAI Sbjct: 375 GIAVQARLAPQQCWQMGDRLWLTFKPDQIHLFDLETGKAI 414 Lambda K H 0.319 0.138 0.387 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: 374 Number of extensions: 21 Number of successful extensions: 4 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