GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuL in Pseudomonas putida KT2440

Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate PP_3180 PP_3180 Smp-30/Cgr1 family protein

Query= uniprot:Q888H2
         (294 letters)



>FitnessBrowser__Putida:PP_3180
          Length = 346

 Score =  134 bits (336), Expect = 4e-36
 Identities = 95/283 (33%), Positives = 142/283 (50%), Gaps = 12/283 (4%)

Query: 14  GESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAADSRGGWIAGMENG 73
           GES VW  R   LY+VDI  G ++      +    +++   +  +A   RG  I   +  
Sbjct: 72  GESLVWDERSGVLYFVDISGGRINGLTPDGEVDCLYESAARIGALALTDRGNLIFTEDAS 131

Query: 74  LYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLMDMAAGAVVGALYR 133
           +           +S   ASV H ++  RFNDG CD QGRF  G  LMD A     GAL+R
Sbjct: 132 VAIFDV--PTRKVSQHSASV-HPRSTYRFNDGACDPQGRFVTG--LMDEALSDNTGALFR 186

Query: 134 YSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDYDTDSGTPHDRRLF 193
           +   Q + +    D+ +P GLA+S DG T+Y  DS  A + I+  +Y  + G      LF
Sbjct: 187 FD-WQLSDQVIHDDMGLPTGLAWSHDGHTVYFVDS--AARAIYRAEYLIE-GRLGAVTLF 242

Query: 194 VDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVPVKKPAMCAFGGPN 253
            +    LGRPDG A+D +G  W+C      + R+  +G L   +++PV  P  C FGGP 
Sbjct: 243 AETPAELGRPDGLALDREGGLWVCQYHGSCLLRYDRHGYLTDQVLMPVPCPTSCCFGGPG 302

Query: 254 LDTLFVTSIR---PGGDLSDQPLAGGVFALRPGVKGLEEPVFQ 293
           ++TL++++ R      DL   P AG ++A+RP   G+    F+
Sbjct: 303 MNTLYISTARYDMTPEDLHHYPDAGDLYAIRPETGGVARHSFK 345


Lambda     K      H
   0.320    0.138    0.441 

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: 366
Number of extensions: 20
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: 294
Length of database: 346
Length adjustment: 28
Effective length of query: 266
Effective length of database: 318
Effective search space:    84588
Effective search space used:    84588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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