Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate Pf1N1B4_2259 Putrescine ABC transporter putrescine-binding protein PotF (TC 3.A.1.11.2)
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2259 Length = 370 Score = 573 bits (1478), Expect = e-168 Identities = 280/366 (76%), Positives = 313/366 (85%), Gaps = 1/366 (0%) Query: 2 MKRFGKTLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYD 61 MK GKTLLA++L G +AG QA D+KVLHVYNWSDYIAPDT++KF E+GIKVVYDV+D Sbjct: 6 MKIAGKTLLAMSLMGVMAGAVQA-DDKVLHVYNWSDYIAPDTVKKFEAESGIKVVYDVFD 64 Query: 62 SNEVLEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVS 121 SNE LEAKLLAGKSGYD+VVPSN+FLAKQIKAGVYQKLDKSKLPNWKNLN DL+ + VS Sbjct: 65 SNETLEAKLLAGKSGYDIVVPSNNFLAKQIKAGVYQKLDKSKLPNWKNLNTDLLKAVSVS 124 Query: 122 DPGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSP 181 DPGNEHA PYMWG+IGIG+NPDKVKAA G +AP +SWDL+FKPEN KLK CG+SFLDSP Sbjct: 125 DPGNEHAFPYMWGSIGIGFNPDKVKAALGADAPTNSWDLLFKPENAAKLKSCGISFLDSP 184 Query: 182 TEILPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGY 241 TE++P ALHYLGY D+ + K+L AE LFLKIRP V YFHSSKYISDLANGNICVA+GY Sbjct: 185 TEMIPVALHYLGYPTDSQDKKQLAEAEALFLKIRPSVGYFHSSKYISDLANGNICVAVGY 244 Query: 242 SGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEI 301 SGDIYQAK+RA EA +KV V YNIPKEGAGSF+DMVAIPKDAEN EGA F+ FL KPEI Sbjct: 245 SGDIYQAKARAAEAGDKVKVSYNIPKEGAGSFYDMVAIPKDAENVEGAYKFMTFLQKPEI 304 Query: 302 MAEITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWT 361 MAEIT+ V+FPNGNAAATPLV + I DPGIYP EV+ KLY DLPA TQR +TRSWT Sbjct: 305 MAEITNAVRFPNGNAAATPLVEKEITADPGIYPPAEVLAKLYAIADLPAATQRILTRSWT 364 Query: 362 KIKSGK 367 KIKSGK Sbjct: 365 KIKSGK 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: 600 Number of extensions: 22 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