Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 171 bits (433), Expect = 3e-47 Identities = 94/264 (35%), Positives = 157/264 (59%), Gaps = 19/264 (7%) Query: 19 LLEIRNLTKSY--DGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQI 76 ++ ++++K+Y G A+ VSL++ GE+F ++GASG GKSTL+R++ G E PSAGQ+ Sbjct: 1 MITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQV 60 Query: 77 MLDGVDLSQVP-----PYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVN 131 ++DG D++ + R + M+FQ + L TV QN+AF LK P AE+ +R Sbjct: 61 IVDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAFPLKLAGRPAAEVKARTA 120 Query: 132 EMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLE 191 E+L V + A + P QLSGGQ+QRV +AR+LA PK+LL DE ALD + +++ Sbjct: 121 ELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILDL 180 Query: 192 VVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIG 251 + + +G+T V++TH+ + + R+A+++ G+ V+ G EE++ HP + + F+ Sbjct: 181 IAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFV- 239 Query: 252 SVNVFEGVLKERQEDGLVLDSPGL 275 R+ +G V +PG+ Sbjct: 240 -----------REAEGDVTAAPGV 252 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: 314 Number of extensions: 15 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: 377 Length of database: 332 Length adjustment: 29 Effective length of query: 348 Effective length of database: 303 Effective search space: 105444 Effective search space used: 105444 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