Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 114 bits (286), Expect = 3e-30 Identities = 65/193 (33%), Positives = 109/193 (56%), Gaps = 17/193 (8%) Query: 24 KFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGY---NIWKNK 80 K A+ +VSL++N+G+ +LG SG GKTTL R++ G + PT G ++ DG N+ NK Sbjct: 26 KLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILIDGQDISNVPPNK 85 Query: 81 RKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKL 140 R + ++ Y+ P + + L+ + + K E R+ LELV+L Sbjct: 86 RPVNMVFQS---------YAVFPHMTVADNVAYG--LKVDNVPKAEREARVAEALELVQL 134 Query: 141 TPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIK 200 G+ P QLSGGQ+QR+++AR+L PR+++ DEP++ +DA LR + L ++ Sbjct: 135 GGLG---GRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQ 191 Query: 201 NRLNLTMVFITHD 213 ++ +T + +THD Sbjct: 192 EKVGITFIMVTHD 204 Lambda K H 0.321 0.141 0.410 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: 253 Number of extensions: 10 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: 324 Length of database: 381 Length adjustment: 29 Effective length of query: 295 Effective length of database: 352 Effective search space: 103840 Effective search space used: 103840 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