Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 286 bits (732), Expect = 7e-82 Identities = 169/373 (45%), Positives = 229/373 (61%), Gaps = 30/373 (8%) Query: 14 GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIGERSVLGVHPK 73 GEV L GI++ + GEF+V++G SGCGKSTLL ++AGL PS G I +G+R V + K Sbjct: 45 GEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAK 104 Query: 74 DRDIAMVFQSYALYPNLSVARNIGFGLEM---------------RRVP---------QAE 109 RDIAMVFQSYALYP+LSV N+ FGL R +P +A Sbjct: 105 ARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEAR 164 Query: 110 HDKAVRDTARLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLR 169 + VR+ A +LQ++ LLDR+P QLSGGQ+QRVA+GRA+ RNPQVFL DEPLSNLDAKLR Sbjct: 165 IKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLR 224 Query: 170 MEMRTELKRLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLY 229 E R ++ L + L T +YVTHDQ EAMT+ RIAV+ G ++Q+A+P E+YDRPA + Sbjct: 225 AETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRF 284 Query: 230 VAGFVGSPPMNILDAEMTANGLKIEGCEEVLPLPAAFNGA--AWAGRRVKVGIRPEALRL 287 VA F+GSPPMN++ + A L++ LP A+ + G+ V++GIRPE L + Sbjct: 285 VAQFIGSPPMNLIPVTVRA-PLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPEHLEV 343 Query: 288 AAGSEAQRLTASVEVVELTGPELVTTATVGSQRIT--ACLPPRTAVGMGSAHAFTFDGTA 345 A + ++ L +V VE G + + I A L P+ MG TF Sbjct: 344 GAAA-SKNLLITVTGVEALGSDTFIAGELKESGIAVQARLAPQQCWQMGDRLWLTFKPDQ 402 Query: 346 LHLFDPESGRSLR 358 +HLFD E+G+++R Sbjct: 403 IHLFDLETGKAIR 415 Lambda K H 0.320 0.136 0.385 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: 389 Number of extensions: 11 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: 360 Length of database: 417 Length adjustment: 30 Effective length of query: 330 Effective length of database: 387 Effective search space: 127710 Effective search space used: 127710 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