Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate BPHYT_RS09400 BPHYT_RS09400 spermidine/putrescine ABC transporter ATPase
Query= TCDB::P31134 (377 letters) >FitnessBrowser__BFirm:BPHYT_RS09400 Length = 359 Score = 263 bits (671), Expect = 7e-75 Identities = 151/357 (42%), Positives = 215/357 (60%), Gaps = 12/357 (3%) Query: 20 LEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLD 79 L ++ ++K Y A++ + L + +GE+ +LLG SGCGK+T L+M+AGF P+ G+I+LD Sbjct: 4 LTLQGISKRYGDFTAIEQLDLAVERGELLSLLGPSGCGKTTTLQMVAGFITPTTGRILLD 63 Query: 80 GVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHM 139 G D++ P R I ++FQSYALFPHMTV N+ FGL+ K+ + E RV E L LV + Sbjct: 64 GRDITNERPEKRGIGVVFQSYALFPHMTVAGNVGFGLEMRKVRRKERDERVAEALSLVRL 123 Query: 140 QEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERV 199 + R P +LSGGQRQRVA+AR++A +P+LLLLDEPM LD KLR+ M +E+ I +R+ Sbjct: 124 KGLGHRYPKELSGGQRQRVAIARAIAMQPELLLLDEPMSNLDAKLREEMHIELRAIQKRL 183 Query: 200 GVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFEGV 259 G+T ++VTHDQ EAMTM+ RIA+M+RG Q+ P + YE P T +++ F+G N F G Sbjct: 184 GITTILVTHDQVEAMTMSDRIAVMHRGVIAQLSTPYDAYERPATPFASTFLGRTNAFSGE 243 Query: 260 LKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNFAVGE 319 + R +D G L V + VD V+V +RPEK+ L ANG G Sbjct: 244 VLRRNPRCAEVDVAGTT--LHVPHEGRHVDGT-VNVYIRPEKVHL-----ANGDARLRGR 295 Query: 320 VIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDSCVVLT 376 + ++G+ + V + G++ AQ H P G EV L W D VLT Sbjct: 296 IATRVFVGNQWLLEVDTELGKLRIAQ----PNHGAPPPEEGHEVGLAWTDDDLRVLT 348 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: 367 Number of extensions: 7 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: 359 Length adjustment: 30 Effective length of query: 347 Effective length of database: 329 Effective search space: 114163 Effective search space used: 114163 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