Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate PP_5181 PP_5181 spermidine/putrescine ABC transporter - periplasmic subunit
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__Putida:PP_5181 Length = 365 Score = 519 bits (1337), Expect = e-152 Identities = 256/367 (69%), Positives = 303/367 (82%), Gaps = 3/367 (0%) Query: 2 MKRFGKTLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYD 61 M + GKTLLA L G++A QA D KVL+VYNWSDYIAPDT+ KF K+TGIKV YDV+D Sbjct: 1 MNKMGKTLLAAALMGAMASAVQAED-KVLNVYNWSDYIAPDTIAKFEKQTGIKVKYDVFD 59 Query: 62 SNEVLEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTL-EV 120 SNE LEAKLLAGKSGYD+VVPSN+FLAKQIKAGVY++LD+SKLPNWKNL+ DL+ + + Sbjct: 60 SNETLEAKLLAGKSGYDIVVPSNNFLAKQIKAGVYEELDRSKLPNWKNLDPDLLKAVGDA 119 Query: 121 SDPGNEHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDS 180 SD N+HA PYMWG+IGIGYNP+KVKAA G + +DSWD+VFKPENI KLK CGVSFLD+ Sbjct: 120 SDKDNKHAFPYMWGSIGIGYNPEKVKAALGVDK-IDSWDVVFKPENIAKLKSCGVSFLDA 178 Query: 181 PTEILPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIG 240 PTE+LPAALHYLG D+ ++LKAAE+LFLKIRP +TYFHSSKYI D+ANGNICVA+G Sbjct: 179 PTEMLPAALHYLGKPTDSTKKEDLKAAEDLFLKIRPSITYFHSSKYIGDMANGNICVAVG 238 Query: 241 YSGDIYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPE 300 YSGD+ Q+K+RA EA +KV V Y IPKEGAG+F+DMVAIPKDAE+ + A F+NFLM+PE Sbjct: 239 YSGDLEQSKARAHEAGDKVKVDYVIPKEGAGTFYDMVAIPKDAEHKDAAYEFMNFLMQPE 298 Query: 301 IMAEITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSW 360 IMAEIT+ V+FPNGNAAATP V + I +DP IYP EV K+LY A QR +TRSW Sbjct: 299 IMAEITNAVRFPNGNAAATPFVDKDITSDPSIYPPAEVKKQLYAIAAPDASVQRVITRSW 358 Query: 361 TKIKSGK 367 TKIKSGK Sbjct: 359 TKIKSGK 365 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: 582 Number of extensions: 15 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: 365 Length adjustment: 30 Effective length of query: 337 Effective length of database: 335 Effective search space: 112895 Effective search space used: 112895 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