Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 302 bits (773), Expect = 1e-86 Identities = 179/387 (46%), Positives = 234/387 (60%), Gaps = 35/387 (9%) Query: 1 MTGLLLKDIRKSY---------GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAG 51 + G++ ++I K + G V V++GI+L+I +GEF+V VGPSGCGKSTLLR++AG Sbjct: 23 VAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAG 82 Query: 52 LEEITGGDMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMR---------- 101 LE + G + + RV+ +P R IAMVFQSYALYPH++VYDN+AFG+R Sbjct: 83 LETPSRGLIKVGDRRVDRLPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQ 142 Query: 102 --------------IARESKEEIDRRVRGAADMLQLTPYLDRLPKALSGGQRQRVAIGRA 147 E + I RRVR A MLQL LDR PK LSGGQ+QRVA+GRA Sbjct: 143 QLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRA 202 Query: 148 ICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIYVTHDQVEAMTLADRIVV 207 I RNP+VFL DEPLSNLDA LR TR +I L ++ TT +YVTHDQ EAMT+ DRI V Sbjct: 203 IARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGVTT-LYVTHDQTEAMTMGDRIAV 261 Query: 208 LSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPATITATGQQTAVSLAGGKSVTLD 267 L+ GH++QV +PLE+Y+RPAN FVA+FIGSP MN+IP T+ A Q T + + Sbjct: 262 LNRGHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLPEAWE 321 Query: 268 VPTNASENGKTASFGVRPEDLRVTEADDFLFEGTVSIVEALGEVTLLYIEGLVENEPIIA 327 P +G+T G+RPE L V A TV+ VEALG T + E + A Sbjct: 322 -PVLRLYDGQTVELGIRPEHLEVGAAASKNLLITVTGVEALGSDTFIAGELKESGIAVQA 380 Query: 328 KMPGIARVGRGDKVRFTADKAKLHLFD 354 ++ GD++ T ++HLFD Sbjct: 381 RLAPQQCWQMGDRLWLTFKPDQIHLFD 407 Lambda K H 0.320 0.137 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: 409 Number of extensions: 19 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: 362 Length of database: 417 Length adjustment: 30 Effective length of query: 332 Effective length of database: 387 Effective search space: 128484 Effective search space used: 128484 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