GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate AO356_28370 AO356_28370 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28370
          Length = 265

 Score =  200 bits (508), Expect = 3e-56
 Identities = 111/241 (46%), Positives = 162/241 (67%), Gaps = 8/241 (3%)

Query: 3   VLKVENLSVHYGM-IQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSG--- 58
           +L+++++ V Y   I AVR VS EV +G+VV L+GANGAGK+T L+  S LVR   G   
Sbjct: 7   ILQIDDIEVLYEQTILAVRSVSLEVEKGQVVVLLGANGAGKSTTLKAASNLVRAERGEVV 66

Query: 59  --KIEFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKK-NREENQAN 115
             +I + G+++ +     + A GL QV EGRH F  LTV ENL  GA  ++  R +  A+
Sbjct: 67  RGRIVYQGKDVTRSAPHTLAASGLVQVLEGRHCFAQLTVEENLLAGALARQVPRRQLLAD 126

Query: 116 LKKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEI 175
           L+ V+  FPRL+ R+   A   SGGEQQM+A+GRALM+ P+L+LLDEPSMGLAP  ++EI
Sbjct: 127 LELVYGHFPRLKLRRKSLAGYTSGGEQQMIAIGRALMARPQLVLLDEPSMGLAPQIVEEI 186

Query: 176 FDIIQDI-QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYL 234
           F+I++ + Q+ G + L+ EQN N AL  +  GYVLE+G++V  G+ ++LA+  +++  YL
Sbjct: 187 FEIVRQLNQRDGVSFLIAEQNINVALRYAHHGYVLESGRVVSEGSAEQLAARSDLQDFYL 246

Query: 235 G 235
           G
Sbjct: 247 G 247


Lambda     K      H
   0.315    0.134    0.358 

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: 155
Number of extensions: 8
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: 236
Length of database: 265
Length adjustment: 24
Effective length of query: 212
Effective length of database: 241
Effective search space:    51092
Effective search space used:    51092
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: 42 (22.0 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