GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Pf1N1B4_3215 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3215
          Length = 255

 Score =  140 bits (354), Expect = 2e-38
 Identities = 88/254 (34%), Positives = 144/254 (56%), Gaps = 26/254 (10%)

Query: 3   VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62
           +LKV +LS+ +G + AV  V+  V E +VVS+IG NGAGKTT+   L+G  +P++G I  
Sbjct: 5   ILKVTDLSMRFGGLLAVNSVALTVKEKQVVSMIGPNGAGKTTVFNCLTGFYQPTAGSIVL 64

Query: 63  LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENL-----------------EMGAFL 105
            G++IQ +P  KI   G+ +  +   +F  +T +ENL                 +  AF 
Sbjct: 65  DGEQIQGLPGHKIALKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFLAGLFKTPAFR 124

Query: 106 KKNREENQAN---LKKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDE 162
           +  RE  +     L+KV      L+E  N+ A TL+ G+Q+ L + R +M+ P++L+LDE
Sbjct: 125 RSEREAMEYAEYWLEKV-----NLKEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDE 179

Query: 163 PSMGLAPIFIQEIFDIIQDIQKQ-GTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGK 221
           P+ GL P   +++  +I  ++++   TVLLIE +    ++ISD  +V+  G  +  GT +
Sbjct: 180 PAAGLNPRETEDLKALIGILREEHDVTVLLIEHDMKLVMSISDHIFVINQGTPLADGTPE 239

Query: 222 ELASSEEVRKAYLG 235
           ++  + EV KAYLG
Sbjct: 240 QIRDNPEVIKAYLG 253


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: 125
Number of extensions: 4
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: 236
Length of database: 255
Length adjustment: 24
Effective length of query: 212
Effective length of database: 231
Effective search space:    48972
Effective search space used:    48972
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