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::Q70HW1 (384 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 194 bits (492), Expect = 4e-54 Identities = 102/223 (45%), Positives = 137/223 (61%), Gaps = 4/223 (1%) Query: 19 PTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRD 78 P + +L+I D E +GPSG GKTT LR IAGLE G + + V R Sbjct: 16 PALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFDGQDVTYASAAARR 75 Query: 79 IAMVFQNYALYPHMTVYQNMAFGLKLRK----VPKAEIDRRVQEAAKILDIAHLLDRKPK 134 + VFQ YAL+ HMTV +N+AFGL +RK KAEI RRV+E K++++ L R P Sbjct: 76 VGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLKLVELEGLGGRYPS 135 Query: 135 ALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTH 194 LSGGQRQRVAL RA+ +P V L+DEP LDA +R +R E+R++H T I+VTH Sbjct: 136 QLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRVHDATGVTTIFVTH 195 Query: 195 DQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIG 237 DQ EA+ + DR+ ++ +G I+Q TP V+ P+ FV GF+G Sbjct: 196 DQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVG 238 Lambda K H 0.321 0.138 0.395 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: 353 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: 384 Length of database: 339 Length adjustment: 29 Effective length of query: 355 Effective length of database: 310 Effective search space: 110050 Effective search space used: 110050 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