Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate WP_004307355.1 C665_RS09750 polyamine ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >NCBI__GCF_000310185.1:WP_004307355.1 Length = 362 Score = 270 bits (691), Expect = 3e-77 Identities = 144/367 (39%), Positives = 223/367 (60%), Gaps = 5/367 (1%) Query: 1 MMKRFGKTLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVY 60 M +FG + L LA AG A AA+ +L+VYNW+DYIA DT+ F K +GI+V YD+Y Sbjct: 1 MTLKFG-WMAVLALA---AGAAVAAEEPILNVYNWNDYIAADTIPAFEKASGIEVRYDLY 56 Query: 61 DSNEVLEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEV 120 DSN L+ KLL G SGYDVV PS + KQI+AG++Q LDKS+LPN +++ ++ + V Sbjct: 57 DSNATLQGKLLTGGSGYDVVYPSVEYAGKQIQAGIFQPLDKSRLPNLVHIDPLILEAVAV 116 Query: 121 SDPGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDS 180 +DPGN + +PYMW TIG+ N DKV A P ++WDL+F P +LK CG++ +D Sbjct: 117 ADPGNRYLVPYMWFTIGVAINVDKVMKALDGKLPDNAWDLLFDPALTARLKGCGIALMDE 176 Query: 181 PTEILPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIG 240 ++++PAA+ G P +P +++AA E +R + F+++ I +A G++CVA+ Sbjct: 177 ASDVIPAAMLDAGLDPVKMDPADIRAAVEHIRPVRKDIRSFNTAP-IEQMAKGSLCVAMM 235 Query: 241 YSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPE 300 +SGD A RA+ ++V ++Y IP GA D++AIP+DA + A +++ +M P Sbjct: 236 FSGDARIAARRAQIGGSEVRLQYLIPAVGAMMSVDVMAIPRDAPHPHNAHRWIDAMMDPA 295 Query: 301 IMAEITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSW 360 +A I++ + + N AA L +R+DP I E V + L P L QR +T++ Sbjct: 296 TVARISNETFYISANTAALALTDATLRDDPAINVPEAVKRTLRAKPVLGKDVQRELTQAL 355 Query: 361 TKIKSGK 367 + K+ + Sbjct: 356 NRFKAAR 362 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: 341 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: 362 Length adjustment: 29 Effective length of query: 338 Effective length of database: 333 Effective search space: 112554 Effective search space used: 112554 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 24 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