Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate BPHYT_RS32845 BPHYT_RS32845 ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__BFirm:BPHYT_RS32845 Length = 372 Score = 362 bits (929), Expect = e-105 Identities = 175/359 (48%), Positives = 244/359 (67%), Gaps = 1/359 (0%) Query: 8 TLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLE 67 T+L A + A+AAD L+VYNWSDYIA DT+ F K++G+ V YD YDS++ L+ Sbjct: 14 TMLCSLTALTAMNAARAADTS-LNVYNWSDYIAKDTIANFEKQSGVTVKYDSYDSDDTLQ 72 Query: 68 AKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEH 127 AKLLAG SGYD+VVP++S++A+QI+AGVYQK+DKSK+PN NL+ LM + +DPGN++ Sbjct: 73 AKLLAGSSGYDIVVPTSSYMARQIEAGVYQKIDKSKMPNLANLDPGLMKLIADADPGNQY 132 Query: 128 AIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPA 187 +P+ WGT GIGYN VK A G APVDSW L+F P N+ K+K CGVSFLDS ++ PA Sbjct: 133 GVPWAWGTDGIGYNVQAVKQALGGEAPVDSWSLLFDPANLSKVKSCGVSFLDSAADVFPA 192 Query: 188 ALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQ 247 L Y+ P++ NP + +AA E+ K+RPY+T F+SS YI+DLAN +ICVA G+SGD+ Sbjct: 193 VLQYMHKNPNSTNPGDYQAAYEVLKKVRPYITQFNSSGYINDLANNDICVAFGFSGDVGI 252 Query: 248 AKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITD 307 A+ RA EAK V+++ K+ + D++ IPKDA + E A+ ++N++ P++ AEIT+ Sbjct: 253 ARRRASEAKRTYEVRFSNIKDAGLVWMDVMVIPKDAPHPEAAMKWMNYIEDPKVSAEITN 312 Query: 308 VVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSG 366 V +P N AA V+ AI D +YP E V+ K+ PA R R W ++KSG Sbjct: 313 EVFYPTANRAARQFVTPAIEQDANVYPPEAVLNKMTLMRPQPAPIMRLENRLWAQLKSG 371 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: 446 Number of extensions: 21 Number of successful extensions: 1 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: 372 Length adjustment: 30 Effective length of query: 337 Effective length of database: 342 Effective search space: 115254 Effective search space used: 115254 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