GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potD in Pseudomonas putida KT2440

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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