Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate PfGW456L13_928 Putrescine ABC transporter putrescine-binding protein PotF (TC 3.A.1.11.2)
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_928 Length = 370 Score = 568 bits (1463), Expect = e-166 Identities = 276/365 (75%), Positives = 311/365 (85%), Gaps = 1/365 (0%) Query: 3 KRFGKTLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDS 62 K GKTLLA+++ G +AG QA D+KVLHVYNWSDYIAPDT++KF E+GIKVVYDV+DS Sbjct: 7 KLAGKTLLAMSVMGLMAGAVQA-DDKVLHVYNWSDYIAPDTVKKFEDESGIKVVYDVFDS 65 Query: 63 NEVLEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSD 122 NE LEAKLLAGKSGYD+VVPSN+FLAKQIKAGVYQKLDKSKLPNWKNLN DL+ + VSD Sbjct: 66 NETLEAKLLAGKSGYDIVVPSNNFLAKQIKAGVYQKLDKSKLPNWKNLNTDLLKAVSVSD 125 Query: 123 PGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPT 182 PGNEHA PYMWG+IGIG+NP+KVKA G +AP +SWDL+FKPEN KLK CG+SFLDSPT Sbjct: 126 PGNEHAFPYMWGSIGIGFNPEKVKAVLGADAPTNSWDLLFKPENAAKLKACGISFLDSPT 185 Query: 183 EILPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYS 242 E++P ALHYLGY D+ + K+L AE LFLKIRP V YFHSSKYISDLANGNICVA+GYS Sbjct: 186 EMIPVALHYLGYPTDSQDKKQLAEAEALFLKIRPSVGYFHSSKYISDLANGNICVAVGYS 245 Query: 243 GDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIM 302 GDIYQAKSRAEEA KV V YNIPKEGAGSF+DMVAIPKDAEN EGA F+ FL KPEIM Sbjct: 246 GDIYQAKSRAEEAGGKVKVSYNIPKEGAGSFYDMVAIPKDAENVEGAYKFMTFLQKPEIM 305 Query: 303 AEITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTK 362 AEIT+ V+FPNGNAAAT LV + I +DPG+YP +V+ KLY DLPA TQR MTRSWTK Sbjct: 306 AEITNAVRFPNGNAAATALVDKDITSDPGVYPPADVLAKLYAIADLPAATQRIMTRSWTK 365 Query: 363 IKSGK 367 IKSGK Sbjct: 366 IKSGK 370 Lambda K H 0.315 0.133 0.390 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: 598 Number of extensions: 19 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: 367 Length of database: 370 Length adjustment: 30 Effective length of query: 337 Effective length of database: 340 Effective search space: 114580 Effective search space used: 114580 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: 42 (22.0 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