Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate 8502259 DvMF_2969 ABC transporter related (RefSeq)
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Miya:8502259 Length = 418 Score = 248 bits (634), Expect = 2e-70 Identities = 130/313 (41%), Positives = 193/313 (61%), Gaps = 5/313 (1%) Query: 2 NDAIPRPQAKTRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTL 61 +DA P + + L + L K ++ AV+DVS + +G F++LG SGCGK+TL Sbjct: 11 SDAFPNASPVASPSASADLSVTRLVKRFEKFTAVNDVSFEVEQGRFFSILGPSGCGKTTL 70 Query: 62 LRMLAGFEQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKL 121 LRM+AGFE P +G I + G D++ + P RP+N++FQ ALFP M+V +N+AFGLK+ + Sbjct: 71 LRMIAGFESPDSGVIAIRGRDMAGIAPNRRPVNLIFQHLALFPMMSVAENVAFGLKRRGM 130 Query: 122 PKAEIASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALD 181 EI+ RV ++L V + + + P QLSGGQ+QRVA+AR L P +LLLDEP+GALD Sbjct: 131 AGGEISRRVQDVLERVGLPGYGVKMPAQLSGGQKQRVAIARCLVLEPAVLLLDEPLGALD 190 Query: 182 KKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHP 241 KLR++M++E+ + VG T V +THDQ EA+ M+ +A+MN G+F Q+ P +Y P Sbjct: 191 LKLREQMKVELKTLQAEVGTTFVYITHDQSEALVMSDHVAVMNAGRFEQVDTPRNLYRRP 250 Query: 242 TTRYSAEFIGSVNVFEGVLKERQED-GLVLDSPGLVHPLKVDADASVVDNVPVHVALRPE 300 + + A F+G NV+ G L+E D GLV G V +V A + V + +RPE Sbjct: 251 ASAFVAGFVGETNVWSGTLEEATGDAGLVRTDEGAVFRARV--AAGLAKGTRVDMFIRPE 308 Query: 301 KIMLCEEPPANGC 313 +++ +P C Sbjct: 309 AVLI--DPDGASC 319 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: 361 Number of extensions: 14 Number of successful extensions: 1 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: 418 Length adjustment: 31 Effective length of query: 346 Effective length of database: 387 Effective search space: 133902 Effective search space used: 133902 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: 50 (23.9 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