Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate WP_011385005.1 AMB_RS13210 polyamine ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >NCBI__GCF_000009985.1:WP_011385005.1 Length = 369 Score = 363 bits (931), Expect = e-105 Identities = 197/370 (53%), Positives = 252/370 (68%), Gaps = 8/370 (2%) Query: 4 RFGKTLLALTL----AGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDV 59 R T +A++L SV+G AQAA++KVL+VYNWSDYIAPDTLEKFT TGIKV YDV Sbjct: 2 RISFTAVAVSLIAAAVSSVSG-AQAAEDKVLNVYNWSDYIAPDTLEKFTALTGIKVNYDV 60 Query: 60 YDSNEVLEAKLLAGKSGYDVVVPSNS-FLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTL 118 YDSNEVL+AKL AGKSGYDVV PS S FLA QIKAG+Y+KLD+SKL N+ NL+ +M TL Sbjct: 61 YDSNEVLQAKLQAGKSGYDVVFPSASPFLANQIKAGIYRKLDRSKLSNYGNLDAQVMVTL 120 Query: 119 E-VSDPGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSF 177 +DPGN +AIPY G YN DKV A G + P+DSW +F P + KLK CGVS Sbjct: 121 NRAADPGNLYAIPYAISPTGFAYNVDKVAKA-GKDMPLDSWAALFDPAQVAKLKGCGVSL 179 Query: 178 LDSPTEILPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICV 237 LD+PTE+ PAAL YLG + + +LKAA E K+RP + YFHSSK+I+DLANG+IC+ Sbjct: 180 LDAPTEVFPAALTYLGKNGASLDSADLKAAAEAVTKVRPSIKYFHSSKFINDLANGDICM 239 Query: 238 AIGYSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLM 297 A GY GD+ Q+++RA EA V +K IPKEGA D + IP DA + E A F++F+M Sbjct: 240 AHGYVGDLVQSRNRAAEAGKGVNIKIVIPKEGAVINIDSMVIPADAPHPENAHKFIDFMM 299 Query: 298 KPEIMAEITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMT 357 K E+ A ++ + N + L+ + I+ DP I+PSE+V KLY P +R T Sbjct: 300 KQEVAAGFSNTTGYGNPIPGSRSLIRKEIQEDPVIFPSEQVTAKLYQVPPADMAKERERT 359 Query: 358 RSWTKIKSGK 367 R WT +K+G+ Sbjct: 360 RLWTTVKTGR 369 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: 459 Number of extensions: 24 Number of successful extensions: 4 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: 369 Length adjustment: 30 Effective length of query: 337 Effective length of database: 339 Effective search space: 114243 Effective search space used: 114243 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