GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pseudomonas putida KT2440

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PP_2767 PP_2767 putative Branched-chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__Putida:PP_2767
          Length = 277

 Score =  196 bits (498), Expect = 5e-55
 Identities = 117/269 (43%), Positives = 164/269 (60%), Gaps = 19/269 (7%)

Query: 9   MSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTM 68
           MS+  LL++E +S+ F G+ AI+D  F    G+I ALIGPNGAGK+++ N I G Y+   
Sbjct: 1   MSNLPLLELEGISLSFKGVKAISDIGFSVAEGEICALIGPNGAGKSSLLNIINGVYRAQQ 60

Query: 69  GMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKAS 128
           G I F   +G+Q    R+          +ARTFQNI LF G++VL+N+L  ++  L + S
Sbjct: 61  GRIRF---AGQQ---RRVMHPHAAARDGIARTFQNIALFKGMSVLDNVLTGRN--LKRRS 112

Query: 129 GYTILGL-IGVGP----YKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIA 183
            +    L IG  P     +R AAE +      +E   +    D+  G LPYG Q+R+E+A
Sbjct: 113 SWLEQALRIGRAPGEDDRQRAAAERV------IEFLRIQPWRDEIVGTLPYGLQKRIELA 166

Query: 184 RAMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVV 243
           RA+   P LL LDEP AG+N  E   ++  +  I  E G +++LIEHD+ VVM IS HVV
Sbjct: 167 RALAAEPRLLLLDEPMAGMNAEEKREMSRFIVEINREFGMTVVLIEHDIGVVMGISHHVV 226

Query: 244 VLEYGQKISDGTPDHVKNDPRVIAAYLGV 272
           VL+YG+KI DG+P+ V+ +P VIAAYLGV
Sbjct: 227 VLDYGRKIGDGSPEQVRRNPDVIAAYLGV 255


Lambda     K      H
   0.318    0.136    0.386 

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: 183
Number of extensions: 9
Number of successful extensions: 3
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: 292
Length of database: 277
Length adjustment: 26
Effective length of query: 266
Effective length of database: 251
Effective search space:    66766
Effective search space used:    66766
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: 41 (21.7 bits)
S2: 47 (22.7 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