Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate CCNA_01907 CCNA_01907 ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Caulo:CCNA_01907 Length = 253 Score = 132 bits (332), Expect = 1e-35 Identities = 77/216 (35%), Positives = 126/216 (58%), Gaps = 11/216 (5%) Query: 19 LLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIML 78 LL RN+ Y + +++V L+I +G +++G SG GKST LR++ G E P+ G I L Sbjct: 3 LLSFRNVWVEYGDKVVLENVELSIAQGSFVSIVGPSGAGKSTFLRLVIGQEAPTRGAIDL 62 Query: 79 DGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLK------QDKLPKAEIASRVNE 132 +G +L P R + +FQ Y++FPH++ N+ FGL + KL A+ + + + Sbjct: 63 EGRNLRAEPGPDRGV--VFQKYSVFPHLSARDNVVFGLDCAGSALRGKLSGAKRRAALEQ 120 Query: 133 ---MLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQ 189 ML V + + P ++SGG +QR+A+A++L K+P++LLLDEP GALD +R M Sbjct: 121 ADAMLAAVGLGDSGDLYPAKMSGGMQQRLAIAQALIKKPRILLLDEPFGALDPGVRLDMH 180 Query: 190 LEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNR 225 + + G+T +MVTHD +EA + R+ ++ Sbjct: 181 ELITSLWRDNGLTIMMVTHDIKEAFKLGTRVLAFDK 216 Lambda K H 0.321 0.137 0.400 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: 209 Number of extensions: 9 Number of successful extensions: 3 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: 377 Length of database: 253 Length adjustment: 27 Effective length of query: 350 Effective length of database: 226 Effective search space: 79100 Effective search space used: 79100 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: 48 (23.1 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