GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braG in Pseudomonas fluorescens FW300-N2E3

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AO353_13360 AO353_13360 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_13360 AO353_13360 ABC
           transporter ATP-binding protein
          Length = 238

 Score =  278 bits (710), Expect = 9e-80
 Identities = 144/236 (61%), Positives = 182/236 (77%), Gaps = 1/236 (0%)

Query: 9   QPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSV 68
           QP+L++  ++ +YG I+AL  V +H+N+GE VSLIG+NGAGKSTL+M+I G P+A  G +
Sbjct: 3   QPILELKAIDVFYGPIQALKKVSLHINEGETVSLIGSNGAGKSTLLMSIFGQPRAAGGQI 62

Query: 69  VFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFT 128
           V+ G DIT   +H IA   IAQSPEGRR+FP MTV ENL MG      ++  ED++++F 
Sbjct: 63  VYRGVDITHKSSHYIASNGIAQSPEGRRVFPDMTVEENLLMGTIPIGDQYATEDMQRMFE 122

Query: 129 LFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRK 188
           LFPRLKER  QR  T+SGGEQQML+I RALM+RPKLLLLDEPSLGLAP++VK IF  +R+
Sbjct: 123 LFPRLKERRNQRAMTMSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFATLRE 182

Query: 189 LNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEG 244
           L    G+T+FLVEQNA  AL+LS RAYVMVNG++ +SG+GKELL N EVR AYL G
Sbjct: 183 L-AGTGMTIFLVEQNANHALKLSDRAYVMVNGEIRLSGTGKELLVNEEVRNAYLGG 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: 238
Number of extensions: 5
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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