Align Putrescine transport system permease protein PotI (characterized)
to candidate GFF3392 PGA1_c34450 putrescine transport system permease protein PotI
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__Phaeo:GFF3392 Length = 271 Score = 295 bits (754), Expect = 1e-84 Identities = 156/276 (56%), Positives = 204/276 (73%), Gaps = 7/276 (2%) Query: 6 VVRSPW-RIVILLLGFTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSA 64 + R W V L LGF FLY PM++L+I+SFN SKLVTVWAG+S +WYGELL+++A ++A Sbjct: 1 MTRLSWFNTVSLTLGFAFLYIPMVILIIFSFNESKLVTVWAGFSVKWYGELLQNEAFLNA 60 Query: 65 VGLSLTIAACAATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLL 124 ++L +A ++T A +LGT+AA VLVR GRF G F+ MI APLVMP+VITGLSLLLL Sbjct: 61 AWVTLKVAVMSSTIATVLGTMAAYVLVRGGRFLGRTLFSGMIYAPLVMPEVITGLSLLLL 120 Query: 125 FVALAHAIGWPADRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKV 184 F+ + DRG++TI LAH TF YV+VV+SSRL DRS+EEAA+DLG + + Sbjct: 121 FIGIG------LDRGVMTIVLAHTTFSMCYVSVVVSSRLVTFDRSLEEAALDLGCSAAEA 174 Query: 185 FFVITLPMIMPAIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINA 244 F ++TLP+I PA+ISGWLLAFTLSLDDLVIASF SGP ATTLP+ +FS+VR+GV+PEINA Sbjct: 175 FRLVTLPIIAPAVISGWLLAFTLSLDDLVIASFTSGPAATTLPIKIFSAVRLGVSPEINA 234 Query: 245 LATLILGAVGIVGFIAWYLMARAEKQRIRDIQRARR 280 L+T+++ V + A + R ++ RD Q A R Sbjct: 235 LSTIMIAIVTLGVVTASLVTKRQLVRQRRDEQNAER 270 Lambda K H 0.330 0.140 0.430 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: 263 Number of extensions: 10 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: 281 Length of database: 271 Length adjustment: 25 Effective length of query: 256 Effective length of database: 246 Effective search space: 62976 Effective search space used: 62976 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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