Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate GFF3390 PGA1_c34430 putrescine transport ATP-binding protein PotG
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Phaeo:GFF3390 Length = 375 Score = 377 bits (967), Expect = e-109 Identities = 193/368 (52%), Positives = 252/368 (68%), Gaps = 6/368 (1%) Query: 8 PQAKTRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAG 67 P+AK PL++ +N+TK + A+DD++L IY+ E FALLG SGCGK+T++RMLAG Sbjct: 12 PEAK------PLIQFQNVTKRFGEFTAIDDLTLGIYEKEFFALLGPSGCGKTTMMRMLAG 65 Query: 68 FEQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIA 127 FE P+ G+I L G D++ VPP R +NMMFQSYALFPH++V NIAFGLK++ PK +IA Sbjct: 66 FETPTEGKIFLSGQDIAPVPPNKRLVNMMFQSYALFPHLSVWDNIAFGLKRENKPKHDIA 125 Query: 128 SRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDR 187 RV EML L +++FA+RKPHQ+SGGQRQRVALARSLAK PKLLLLDEP+GALDKKLR Sbjct: 126 ERVQEMLRLTRLEKFARRKPHQISGGQRQRVALARSLAKAPKLLLLDEPLGALDKKLRQD 185 Query: 188 MQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSA 247 Q E++DI E+ G T V+VTHDQEEAMT+A R+A+M+ G+ VQ+ P+ IYE P + Y A Sbjct: 186 TQFELMDIQEKTGTTFVIVTHDQEEAMTVASRVAVMDNGRIVQVATPDRIYETPNSLYVA 245 Query: 248 EFIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEE 307 +FIG VN+ G + ++ PL V + AS D H+A+RPEK+ + E Sbjct: 246 DFIGDVNIIGGTATPTGPEQYAVNWKDGAAPLTVKSQASFSDGQECHLAIRPEKVTISAE 305 Query: 308 PPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCW 367 PA N G ++ IAYLG++S YHV L SG +I AQ N R + TW D V L W Sbjct: 306 RPAEADNTVQGRILDIAYLGNISTYHVELPSGAVIKAQAANTRRIARRAFTWEDPVWLSW 365 Query: 368 EVDSCVVL 375 + V+L Sbjct: 366 TATAGVLL 373 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: 392 Number of extensions: 13 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: 375 Length adjustment: 30 Effective length of query: 347 Effective length of database: 345 Effective search space: 119715 Effective search space used: 119715 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