GapMind for catabolism of small carbon sources

 

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

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate Pf1N1B4_1379 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:A0A159ZWS6
         (255 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1379
          Length = 290

 Score =  289 bits (739), Expect = 5e-83
 Identities = 150/283 (53%), Positives = 197/283 (69%), Gaps = 30/283 (10%)

Query: 1   MSREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGG 60
           MS  +L V+ L M FGG+ A++ V+L VK   + ALIGPNGAGKTTVFNCLTGFY+ +GG
Sbjct: 1   MSEVVLSVDKLMMHFGGIKALSDVSLKVKRNSIFALIGPNGAGKTTVFNCLTGFYKASGG 60

Query: 61  TILLD------------GEPIQGLP------------------GHHIARKGVVRTFQNVR 90
            I L+            GEP + +                    H I R G+ RTFQN+R
Sbjct: 61  HIELNTRGVKTDVIKMLGEPFKAVDFVSPKSFINRLRYKMFGGTHLINRAGLARTFQNIR 120

Query: 91  LFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFRKSEREAMEYAEYWLDKVNLTEFANRP 150
           LF++M+ +ENLL+AQH  +N    AG+  T  +RK+E +A+++A YWL+ V+L + ANR 
Sbjct: 121 LFREMSVLENLLVAQHMWVNRGMLAGILNTKGYRKAESDALDHAFYWLEVVDLVDCANRL 180

Query: 151 AGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLNPKETEDLKALIGVLREEHNVTVLLI 210
           AG L+YGQQRRLEIAR M TRP+I+ LDEPAAGLNP+ETE L A+I +LR+EH++TV+LI
Sbjct: 181 AGELSYGQQRRLEIARAMCTRPQIICLDEPAAGLNPQETEALSAMIRLLRDEHDLTVVLI 240

Query: 211 EHDMKLVMSISDHIVVINQGTPLADGTPEQIRDNPEVIKAYLG 253
           EHDM +VMSISDHIVV++ G  +A+G PE IR +P+VI AYLG
Sbjct: 241 EHDMGMVMSISDHIVVLDHGVVIAEGGPEAIRHDPKVIAAYLG 283


Lambda     K      H
   0.321    0.138    0.398 

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: 242
Number of extensions: 8
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: 255
Length of database: 290
Length adjustment: 25
Effective length of query: 230
Effective length of database: 265
Effective search space:    60950
Effective search space used:    60950
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: 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:

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