Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate 7025949 Shewana3_3097 extracellular solute-binding protein (RefSeq)
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__ANA3:7025949 Length = 387 Score = 447 bits (1149), Expect = e-130 Identities = 219/367 (59%), Positives = 283/367 (77%), Gaps = 2/367 (0%) Query: 2 MKRFGK-TLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVY 60 MK F K T LAL AG++A +A A+ +V+ VYNWSDYIA DTLE F KETGI+V+YDV+ Sbjct: 22 MKLFNKMTTLALVTAGALASVAAQAE-EVVRVYNWSDYIAEDTLENFKKETGIRVIYDVF 80 Query: 61 DSNEVLEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEV 120 DSNEVLEAKLL+G+SGYD+VVPSN FLAKQIKAG ++ LD+SKL N+KNLN DLM LE Sbjct: 81 DSNEVLEAKLLSGRSGYDIVVPSNHFLAKQIKAGAFKPLDRSKLSNFKNLNADLMKQLEK 140 Query: 121 SDPGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDS 180 +DPGN++A+PY+WGT GIGYN DKVKAA G++AP DS +L+F P+ +K+ +CG + LDS Sbjct: 141 ADPGNQYAVPYLWGTNGIGYNIDKVKAAVGEDAPFDSMELIFNPKYAEKISKCGFAMLDS 200 Query: 181 PTEILPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIG 240 +++P A+ YLG P++ ++ + A EL KIRPYVTYFHSS+YISDLANG+ICVA G Sbjct: 201 ADDMVPQAMIYLGLDPNSTKAEDYEKAGELLEKIRPYVTYFHSSRYISDLANGDICVAFG 260 Query: 241 YSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPE 300 +SGD++QA +RA+EA N + Y+IPKEGA +FDM+AIP DA N E A +N+L++PE Sbjct: 261 FSGDVFQAAARADEAGNGNKIGYSIPKEGANLWFDMLAIPADAANVENAHKLINYLLRPE 320 Query: 301 IMAEITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSW 360 ++A I++ V + N N A PLV EAIRNDP IYP +EV+ KLY P K QR +TR W Sbjct: 321 VIAPISNYVAYANPNDPAQPLVDEAIRNDPAIYPPKEVLDKLYIGEIRPLKIQRVLTRVW 380 Query: 361 TKIKSGK 367 TK+KSG+ Sbjct: 381 TKVKSGQ 387 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: 489 Number of extensions: 14 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: 387 Length adjustment: 30 Effective length of query: 337 Effective length of database: 357 Effective search space: 120309 Effective search space used: 120309 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: 50 (23.9 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