Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate PP_5180 PP_5180 spermidine/putrescine ABC transporter - periplasmic subunit
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__Putida:PP_5180 Length = 364 Score = 437 bits (1124), Expect = e-127 Identities = 216/366 (59%), Positives = 278/366 (75%), Gaps = 10/366 (2%) Query: 5 FGKTLLA---LTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYD 61 F K L+A LTLA SV QAA +H YNWSDYI P TL F K TGIK V DV+D Sbjct: 6 FRKALMAGAGLTLACSV----QAAPT--VHFYNWSDYIGPTTLADFEKATGIKPVQDVFD 59 Query: 62 SNEVLEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVS 121 SNE LE KLLAG +GYDVVVPSN FL KQIKAG +QKLDK+ LPN+ NL+ LM LE + Sbjct: 60 SNETLEGKLLAGNTGYDVVVPSNHFLGKQIKAGAFQKLDKNLLPNYSNLDPALMKRLEKN 119 Query: 122 DPGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSP 181 DPGN++A+PY+WGT GIGYN DKVKAA G + +DSW ++F+PEN++KL +CGV+FLDS Sbjct: 120 DPGNQYAVPYLWGTNGIGYNVDKVKAALGVDT-IDSWAVLFEPENMKKLSKCGVAFLDSA 178 Query: 182 TEILPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGY 241 E+LPA L+Y+G P++ +PK+ AE+ L +RPYVTYFHSSKYI+DLANG+ICVA G+ Sbjct: 179 DEMLPAVLNYMGLNPNSTDPKDYAKAEQKLLAVRPYVTYFHSSKYITDLANGDICVAAGF 238 Query: 242 SGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEI 301 SGD++QAK+RAEEAK V + Y IPKEG +FD++AIPKDA+N + A AF+N+L+KPE+ Sbjct: 239 SGDVFQAKARAEEAKKGVNLAYAIPKEGGNLWFDVLAIPKDAKNVKEAHAFINYLLKPEV 298 Query: 302 MAEITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWT 361 +A+++D V + N N A L+ +A+R D +YP +EV+ K++ +LP K QR MTRSWT Sbjct: 299 IAQVSDYVGYANPNPKAGALMDQAVRTDAAVYPPQEVLDKMFVNSELPPKVQRLMTRSWT 358 Query: 362 KIKSGK 367 K+KSGK Sbjct: 359 KVKSGK 364 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: 491 Number of extensions: 15 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: 364 Length adjustment: 30 Effective length of query: 337 Effective length of database: 334 Effective search space: 112558 Effective search space used: 112558 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