Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate Ga0059261_2703 Ga0059261_2703 ABC-type multidrug transport system, ATPase component
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Korea:Ga0059261_2703 Length = 313 Score = 124 bits (311), Expect = 4e-33 Identities = 87/272 (31%), Positives = 143/272 (52%), Gaps = 9/272 (3%) Query: 16 LTPLLEIRNLTKSY-DGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAG 74 + P+L +R ++K+Y G A+ V L I KGEIFALLG +G GK+TL+ ++ G PS+G Sbjct: 1 MQPILSVRGVSKTYASGHKALGSVDLDINKGEIFALLGPNGAGKTTLISIICGIVTPSSG 60 Query: 75 QIMLDGVDLSQVPPYLR-PINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEM 133 I++DG D P R I ++ Q ++ TV+ + + P + + ++++ Sbjct: 61 TIVVDGHDAISEPRAARMKIGLVPQELSVDMFETVQATTRYSRRLFGRPAND--AYIDQV 118 Query: 134 LGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVV 193 L + + + K +LSGG ++RV +A++LA P +L LDEP +D LR M + Sbjct: 119 LKDLSLYDKRNSKVMELSGGMKRRVLIAKALAHEPDILFLDEPTAGVDVSLRRDMWKLIG 178 Query: 194 DILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSV 253 + ER G T ++ TH EEA MA R+ ++N+G+ + + E+ + R I V Sbjct: 179 SLRER-GTTIILTTHYIEEAEEMADRVGVINKGELLLVEGKAELMKKLGKREMD--IALV 235 Query: 254 NVFEGVLKERQEDGLVLDSPGLVHPLKVDADA 285 + E +E L L+ G H L+ DA Sbjct: 236 EPMTAIPGELEEWHLALEDEG--HRLRYTFDA 265 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: 245 Number of extensions: 14 Number of successful extensions: 4 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: 313 Length adjustment: 29 Effective length of query: 348 Effective length of database: 284 Effective search space: 98832 Effective search space used: 98832 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