Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 199 bits (507), Expect = 7e-56 Identities = 109/256 (42%), Positives = 153/256 (59%), Gaps = 19/256 (7%) Query: 19 PTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRD 78 P + K +LEIADGE L L+GPSG GK+T LR +AGLE G + +DVT+ + R Sbjct: 16 PALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFDGQDVTYASAAARR 75 Query: 79 IAMVFQNYALYPHMTVGENMGFALKIA-GK---SQDEINKRVDEAAATLGLTEFLERKPK 134 + VFQ YAL+ HMTV +N+ F L + GK S+ EI +RV+E + L R P Sbjct: 76 VGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLKLVELEGLGGRYPS 135 Query: 135 ALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTH 194 LSGGQRQRVA+ RA+ P V L+DEP LDA +R R ++ + GVTT++VTH Sbjct: 136 QLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRVHDATGVTTIFVTH 195 Query: 195 DQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIG---------------SP 239 DQ EAL + DR+A+L +G ++Q+G P +++D P FV GF+G + Sbjct: 196 DQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVGEANRFDGQVSGGRFKAG 255 Query: 240 AMNLGTFSVKDGDATS 255 A+ + ++KDG AT+ Sbjct: 256 ALTVPASALKDGAATA 271 Lambda K H 0.316 0.135 0.380 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: 342 Number of extensions: 17 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: 376 Length of database: 339 Length adjustment: 29 Effective length of query: 347 Effective length of database: 310 Effective search space: 107570 Effective search space used: 107570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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