Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate PP_0873 PP_0873 putrescine-binding periplasmic protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__Putida:PP_0873 Length = 359 Score = 426 bits (1094), Expect = e-124 Identities = 202/358 (56%), Positives = 263/358 (73%), Gaps = 5/358 (1%) Query: 9 LLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLEA 68 L L LA SVA A+ + +YNWS Y+APDTL+ F + +GI YDVYDSNE L+ Sbjct: 6 LAPLMLAASVASAAET-----VKIYNWSSYVAPDTLKNFQQASGIVPTYDVYDSNETLDG 60 Query: 69 KLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEHA 128 KL+ G SGYDVV PSN F+A+QI+ ++LDKSKLPNW NLN L+ LEV+DPGN++ Sbjct: 61 KLMTGNSGYDVVFPSNHFMARQIQGKALKRLDKSKLPNWHNLNPVLLKALEVNDPGNQYG 120 Query: 129 IPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAA 188 PY+WG+ GIGYN DKVKA GDNAPVDSWDL+FKPE + KLK CGV+ LD+ E+LP A Sbjct: 121 FPYLWGSTGIGYNIDKVKAVLGDNAPVDSWDLIFKPEYMSKLKSCGVAVLDNGPELLPIA 180 Query: 189 LHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQA 248 LHYLG + +PK+ + A++L +K+RPY++YFHSSKY DLANG+ICV +G+SGD+ QA Sbjct: 181 LHYLGLPHHSQDPKDYEKAKDLLMKVRPYISYFHSSKYTGDLANGDICVVVGFSGDVLQA 240 Query: 249 KSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDV 308 K+RA+EA N V V Y+IPKEGA +FDMVA+P DA + + A++N+L++PE+MA I++ Sbjct: 241 KNRADEANNGVKVGYSIPKEGAPMWFDMVAMPVDAPDEKAGYAYMNYLLQPEVMANISNH 300 Query: 309 VQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSG 366 VQ+ NGN A LV A++ + IYPS+EVM KLY +PAK R TR WT IK+G Sbjct: 301 VQYANGNLKADGLVDPAMKGNTMIYPSDEVMGKLYALEAMPAKIDRIRTRIWTSIKAG 358 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: 500 Number of extensions: 15 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: 359 Length adjustment: 29 Effective length of query: 338 Effective length of database: 330 Effective search space: 111540 Effective search space used: 111540 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