Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 288 bits (738), Expect = 1e-82 Identities = 179/403 (44%), Positives = 230/403 (57%), Gaps = 53/403 (13%) Query: 1 MASVTLRNIRKAYDENE---------VMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAG 51 +A V I K + E V+ INL+IADGEF+V VGPSGCGKSTL+R++AG Sbjct: 23 VAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAG 82 Query: 52 LEDISGGDLTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTK----- 106 LE S G + + RV+ + R IAMVFQSYALYPH+++YDN+AFGL+ G + Sbjct: 83 LETPSRGLIKVGDRRVDRLPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQ 142 Query: 107 ---------------KPEIDAA----VRNAAKILHIDHLLDRKPKQLSGGQRQRVAIGRA 147 +PE +A VR A +L +D LLDR+PKQLSGGQ+QRVA+GRA Sbjct: 143 QLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRA 202 Query: 148 ITRKPKVFLFDEPLSNLDAALRVKMRLEFARLHDELKTTMIYVTHDQVEAMTLADKIVVL 207 I R P+VFL DEPLSNLDA LR + R + L +L T +YVTHDQ EAMT+ D+I VL Sbjct: 203 IARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVL 262 Query: 208 SAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMNFMEGVVQSVTHDGVTVRYE---TGETQ 264 + G+L+QV SP +Y PANRFVA FIGSP MN + VTVR T E Sbjct: 263 NRGHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIP----------VTVRAPLQLTTENF 312 Query: 265 RVAVEPA-----AVKQGDKVTVGIRPEHLHVG-MAEDGISARTMAVESLGDAAYLYAESS 318 R + A + G V +GIRPEHL VG A + VE+LG ++ E Sbjct: 313 RCTLPEAWEPVLRLYDGQTVELGIRPEHLEVGAAASKNLLITVTGVEALGSDTFIAGELK 372 Query: 319 VAPDGLIARIPPLERHTKGETQKLGATPEHCHLFD-SAGKAFQ 360 + + AR+ P + G+ L P+ HLFD GKA + Sbjct: 373 ESGIAVQARLAPQQCWQMGDRLWLTFKPDQIHLFDLETGKAIR 415 Lambda K H 0.320 0.135 0.384 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: 425 Number of extensions: 17 Number of successful extensions: 5 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