Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate PfGW456L13_2830 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2830 Length = 361 Score = 251 bits (640), Expect = 3e-71 Identities = 136/309 (44%), Positives = 195/309 (63%), Gaps = 21/309 (6%) Query: 3 SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62 +++++ ++KR+ L V + +A EF L+GPSGCGK+TLL IAG + ++ Sbjct: 5 TAIEVRNVSKRYSDDPGLAPALDNVSVDIADNEFFTLLGPSGCGKTTLLRTIAGFEHVSD 64 Query: 63 GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122 GEIR+ G+ V +PP R + VFQSYAL+P +SVA NI F LEM+ + + +R+DE+ Sbjct: 65 GEIRLAGEPVNDLPPFKRRVNTVFQSYALFPHMSVAQNIAFGLEMQGLDRKLIPQRVDEM 124 Query: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182 A++Q+ HL R+P++LSGGQ+QRVA+ RALA +P++ L DEPLS LD KLR EM+ E+K Sbjct: 125 LALVQMQHLAKRKPAELSGGQQQRVALARALAPKPKVLLLDEPLSALDLKLRKEMQVELK 184 Query: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSP 242 R+ + +GIT ++VTHDQ EA+TL RIAVM G + Q+G+P+EIY RP + +VA FIG Sbjct: 185 RVQKEAGITFIFVTHDQEEALTLSDRIAVMSAGKILQIGSPNEIYERPQHQFVAQFIGD- 243 Query: 243 TMNLLRGAVTGGQ-----FGIQGAALNLAPPPS--SANEVLLGVRPEHLVMQETAPWRGR 295 +N L G + GQ F G + + P ++V L RPE R Sbjct: 244 -INFLPGHIKRGQQNEKLFVPNGMPVEIPCPAQGFDGSKVQLAFRPE------------R 290 Query: 296 VSVVEPTGP 304 +VEPT P Sbjct: 291 SQLVEPTQP 299 Lambda K H 0.318 0.135 0.388 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: 358 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: 355 Length of database: 361 Length adjustment: 29 Effective length of query: 326 Effective length of database: 332 Effective search space: 108232 Effective search space used: 108232 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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