GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Pseudomonas putida KT2440

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PP_4863 PP_4863 high-affinity branched-chain amino acid transporter, ATP-binding

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__Putida:PP_4863
          Length = 238

 Score =  281 bits (719), Expect = 8e-81
 Identities = 145/235 (61%), Positives = 184/235 (78%), Gaps = 1/235 (0%)

Query: 10  PLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVV 69
           P+L++  ++ +YG I+AL  V +H+N+GE VSLIGANGAGKSTL+M+I G P+A +G +V
Sbjct: 4   PILELKDLDVFYGPIQALKKVSMHINEGETVSLIGANGAGKSTLLMSIFGQPRAASGHIV 63

Query: 70  FEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTL 129
           + G DITR  +H IA   IAQSPEGRR+FP MTV ENL MG      KH  ED+++++ L
Sbjct: 64  YRGTDITRKSSHYIASNGIAQSPEGRRVFPDMTVEENLMMGTIPIGDKHADEDMQRMYEL 123

Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189
           FPRLKER  QR  T+SGGEQQML+I RALM+RPKLLLLDEPSLGLAP++VK IF  +R+L
Sbjct: 124 FPRLKERRNQRAMTMSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFSTLREL 183

Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEG 244
            +  G+T+FLVEQNA  AL+LS RAYVMVNG++ M+G+G+ELL N EVR AYL G
Sbjct: 184 AKT-GMTIFLVEQNANHALKLSDRAYVMVNGQIRMTGTGQELLVNEEVRNAYLGG 237


Lambda     K      H
   0.320    0.137    0.387 

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: 223
Number of extensions: 4
Number of successful extensions: 2
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: 247
Length of database: 238
Length adjustment: 23
Effective length of query: 224
Effective length of database: 215
Effective search space:    48160
Effective search space used:    48160
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: 46 (22.3 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