Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate GFF4210 Psest_4283 Spermidine/putrescine-binding periplasmic protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__psRCH2:GFF4210 Length = 361 Score = 432 bits (1112), Expect = e-126 Identities = 207/360 (57%), Positives = 269/360 (74%), Gaps = 2/360 (0%) Query: 8 TLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLE 67 TL +L +A ++ G A A V H+YNWSDYI TLE+F KETGIK VYDV+DSNE LE Sbjct: 4 TLKSLLVAAAMTGAATAQAASV-HIYNWSDYIGETTLEEFEKETGIKPVYDVFDSNETLE 62 Query: 68 AKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEH 127 KLLAG+SGYDVVVPSN FL KQI+AG +Q LDKSKLPNW++L+ L+ L+ +DPGN H Sbjct: 63 GKLLAGRSGYDVVVPSNHFLGKQIRAGAFQALDKSKLPNWEHLDPALLKQLQKNDPGNAH 122 Query: 128 AIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPA 187 A PY+WGT GIGYN +KVKAA G + +DSW ++F+PEN KL CG++FLDS E++PA Sbjct: 123 AAPYLWGTNGIGYNVEKVKAALGVDE-IDSWSVIFEPENAAKLASCGIAFLDSADEMIPA 181 Query: 188 ALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQ 247 L+YLG P+++N + + AEE L +RP+V YFHSSKYISDLANGNICVA G+SGD++Q Sbjct: 182 MLNYLGLDPNSENAADYQKAEEKLLAVRPHVRYFHSSKYISDLANGNICVAAGFSGDVFQ 241 Query: 248 AKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITD 307 A +RAEEA + + Y IP EGA +FDM+AIP DA N E A AF+N+L++PE++A ++D Sbjct: 242 AAARAEEAGKGIEIAYAIPAEGANLWFDMLAIPADASNVEEAHAFINYLLRPEVIAAVSD 301 Query: 308 VVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSGK 367 V + N N A L+ + +R D +YP +EV+ +LY +LP K QR MTR+WTK+KSGK Sbjct: 302 YVGYANPNLKAGELMDQEVREDASVYPPQEVLDRLYVSAELPPKIQRLMTRTWTKVKSGK 361 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: 457 Number of extensions: 20 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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