GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Pseudomonas putida KT2440

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate PP_2748 PP_2748 putative Branched-chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::Q8DQH8
         (254 letters)



>lcl|FitnessBrowser__Putida:PP_2748 PP_2748 putative Branched-chain
           amino acid ABC transporter, ATP-binding protein
          Length = 266

 Score =  193 bits (490), Expect = 3e-54
 Identities = 98/250 (39%), Positives = 148/250 (59%)

Query: 2   ALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVT 61
           ALLEV+ ++  F G+ A+ D++  +  GE+  LIGPNGAGK++L N+L GVY    G + 
Sbjct: 13  ALLEVRNVSLSFKGVKAISDLSFSVRRGEICALIGPNGAGKSSLLNILNGVYRADAGQLF 72

Query: 62  LDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAF 121
                L    P + A LG+GRTFQN  LFK ++VLDN+L       + +     L LP  
Sbjct: 73  FATEPLRRPHPLQAARLGIGRTFQNNALFKKMSVLDNLLTGLSRFQRSYFLEQALGLPRA 132

Query: 122 YKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAG 181
            +  +    +A ++L   +L    +    +L+YG Q+R+E+ RAL  +P +L LDEP AG
Sbjct: 133 RREARAFAERAEQVLAFLELQPWRDVAVGSLAYGLQKRVELGRALIAQPTLLLLDEPMAG 192

Query: 182 MNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKT 241
           MN +E  +++  I  I  +   T++LIEHD+ +VM ++  + VL+YGR +  GTP E++ 
Sbjct: 193 MNAEEKQDMSRFIADINRDLGTTVILIEHDIQVVMGLSSHVVVLDYGRKVGDGTPAEVQA 252

Query: 242 NKRVIEAYLG 251
           N  VI AYLG
Sbjct: 253 NPDVIAAYLG 262


Lambda     K      H
   0.319    0.139    0.385 

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: 152
Number of extensions: 2
Number of successful extensions: 1
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: 254
Length of database: 266
Length adjustment: 24
Effective length of query: 230
Effective length of database: 242
Effective search space:    55660
Effective search space used:    55660
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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