Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate Ga0059261_2250 Ga0059261_2250 ABC-type multidrug transport system, ATPase component
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Korea:Ga0059261_2250 Length = 307 Score = 132 bits (331), Expect = 2e-35 Identities = 81/212 (38%), Positives = 123/212 (58%), Gaps = 5/212 (2%) Query: 20 LEIRNLTKSYDG-QHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIML 78 +EI L+K Y G + A+DDVS T+ +G+IF LLG +G GKSTL+ +LAG +AG+ + Sbjct: 6 IEIEGLSKVYQGGKQALDDVSFTVPRGQIFGLLGPNGAGKSTLINILAGLVNKTAGRASI 65 Query: 79 DGVDLSQVPPYL-RPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLV 137 G D+ Q P R I ++ Q P T + + +PKA+ R E+L V Sbjct: 66 WGFDIDQHPRNAKRAIGIVNQEILFDPFFTPVETLEIQAGLYGVPKAQ--RRSMELLRAV 123 Query: 138 HMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILE 197 H+++ A LSGG ++R+ +A+++ P +L+LDEP +D +LR ++ V + E Sbjct: 124 HLEDKAHAYSRTLSGGMKRRLMVAKAMVHSPPVLVLDEPTAGVDIELRQQLWAYVRSLNE 183 Query: 198 RVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFV 229 R GVT V+ TH EEA + RIAI+N GK + Sbjct: 184 R-GVTVVLTTHYLEEAEELCDRIAIINHGKLI 214 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: 284 Number of extensions: 15 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: 307 Length adjustment: 28 Effective length of query: 349 Effective length of database: 279 Effective search space: 97371 Effective search space used: 97371 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