Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= reanno::pseudo5_N2C3_1:AO356_00010 (365 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 214 bits (546), Expect = 2e-60 Identities = 131/301 (43%), Positives = 180/301 (59%), Gaps = 18/301 (5%) Query: 3 TLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTIEL 62 T+ I +++K F + +DLE+ D E + +GPSG GK+TLLR IAGLE +G + Sbjct: 2 TIAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLF 61 Query: 63 DGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLA-GEKKP---DVERKVAEAA 118 DG+D+T + A R + VFQ YAL+ HMTV KN++F LD+ G+ KP ++ R+V E Sbjct: 62 DGQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELL 121 Query: 119 RILELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSR 178 +++EL L R P QLSGGQRQRVA+ RA+ P + L DEP LDA +R R EL R Sbjct: 122 KLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRR 181 Query: 179 LHKELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPK 238 +H T I+VTHDQ EA+ LA +V +LN GRIEQIG+P +++ P FV GF+G Sbjct: 182 VHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVG--- 238 Query: 239 MGFLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLGAEG-QVL 297 +A SG RF +G L +P +SAL G + T +RP L G +VL Sbjct: 239 ----EANRFDGQVSG--GRFKAG-ALTVP--ASALKDG-AATAYVRPHDFALDEAGFEVL 288 Query: 298 V 298 + Sbjct: 289 I 289 Lambda K H 0.319 0.136 0.381 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: 317 Number of extensions: 11 Number of successful extensions: 2 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: 365 Length of database: 339 Length adjustment: 29 Effective length of query: 336 Effective length of database: 310 Effective search space: 104160 Effective search space used: 104160 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: 49 (23.5 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