Align ABC transporter related (characterized, see rationale)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 132 bits (331), Expect = 1e-35 Identities = 84/230 (36%), Positives = 126/230 (54%), Gaps = 17/230 (7%) Query: 27 ISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLAGEELKMKRRGDGKLQPSD 86 +S + G+++ ++G SG GK+T LR + E+ GS+ LAGE + +R L P Sbjct: 27 VSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQRS---LPPET 83 Query: 87 RRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSRAESVEEAEALLAKVGLAE 146 R +GMVFQ++ L+ H+TVL+N+ G R R S A LA VGL Sbjct: 84 R--------SVGMVFQDYALFPHLTVLDNVCFG-----LRDRKGSAAVARQALALVGLEG 130 Query: 147 KRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPELVGEVLRVMRSLAEEGR- 205 YP LSGGQQQRVA+ARALA P ++L DEP S LD ++ + + +R + + + Sbjct: 131 LERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQA 190 Query: 206 TMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSDRFRQFVS 255 T ++VTH+ A + +RV + G+ E G P+E+F S +F+S Sbjct: 191 TAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLS 240 Lambda K H 0.318 0.133 0.377 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: 211 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: 263 Length of database: 368 Length adjustment: 27 Effective length of query: 236 Effective length of database: 341 Effective search space: 80476 Effective search space used: 80476 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 (21.7 bits) S2: 48 (23.1 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