Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate GFF3389 PGA1_c34420 putrescine-binding periplasmic protein PotF
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__Phaeo:GFF3389 Length = 361 Score = 380 bits (976), Expect = e-110 Identities = 194/359 (54%), Positives = 249/359 (69%) Query: 8 TLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLE 67 TL +TL VA + AA + + VYNWSDYI D LEKF ETGI ++YDV+DSNE+LE Sbjct: 2 TLKTMTLTAIVALSSAAAVAEEVRVYNWSDYIDEDLLEKFETETGIDLIYDVFDSNELLE 61 Query: 68 AKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEH 127 K+LAG SGYDVVVP+ SFLA+QI+AG +QKLD SKL N N+ + DP N + Sbjct: 62 TKMLAGGSGYDVVVPTGSFLARQIQAGAFQKLDTSKLSNAGNMWDVIEDRTARYDPDNLY 121 Query: 128 AIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPA 187 ++ YMWGT GIG N KV+ A G +AP+DS +LVF P+NI+KL CGV FLD+P E++PA Sbjct: 122 SVNYMWGTTGIGANTAKVEEALGADAPIDSLELVFNPDNIEKLANCGVYFLDAPDEMIPA 181 Query: 188 ALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQ 247 AL Y+G P++ +P + AE + + IRPYV FHSS+YI+ LANG+ICVA G+SGDI Q Sbjct: 182 ALKYIGEDPNSMDPDVVAKAEPVLMAIRPYVKKFHSSEYINALANGDICVAFGWSGDILQ 241 Query: 248 AKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITD 307 A+ RA+EA N V + +N PKEGA +FD +AIP DA N +GA F+NF+M+ E MA ++ Sbjct: 242 ARDRADEADNGVEIVFNAPKEGALMWFDQMAIPVDAPNPDGAHKFLNFIMEAENMAAASN 301 Query: 308 VVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSG 366 V + NGN A+ + E + DP IYPSEE +K LY P K QR TR WTKIKSG Sbjct: 302 YVYYANGNKASQEFLEEDVIGDPAIYPSEETLKNLYIKEAYPPKVQRKATRMWTKIKSG 360 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: 452 Number of extensions: 17 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: 361 Length adjustment: 29 Effective length of query: 338 Effective length of database: 332 Effective search space: 112216 Effective search space used: 112216 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