GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Pf1N1B4_3215 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3215
          Length = 255

 Score =  119 bits (299), Expect = 4e-32
 Identities = 79/257 (30%), Positives = 138/257 (53%), Gaps = 24/257 (9%)

Query: 6   NKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGN 65
           ++ +L+V  L + +GG+ AV  V   V+E ++VS+IG NGAGKTT    +TG      G+
Sbjct: 2   SREILKVTDLSMRFGGLLAVNSVALTVKEKQVVSMIGPNGAGKTTVFNCLTGFYQPTAGS 61

Query: 66  IEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKM 125
           I   G+ I+G     +  +G+V   +   +F  MT  ENL +  + R      LA + K 
Sbjct: 62  IVLDGEQIQGLPGHKIALKGVVRTFQNVRLFKDMTAVENLLIAQH-RHLNTNFLAGLFKT 120

Query: 126 FTIFPR-----------------LRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDE 168
              F R                 L+E  ++ AGT++ G+Q+ L + R +M++P++L+LDE
Sbjct: 121 -PAFRRSEREAMEYAEYWLEKVNLKEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDE 179

Query: 169 PSMGLSPIMVD---KIFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGP 225
           P+ GL+P   +    +  ++R+ +   VT++L+E +    ++I+D  +V+  G     G 
Sbjct: 180 PAAGLNPRETEDLKALIGILREEH--DVTVLLIEHDMKLVMSISDHIFVINQGTPLADGT 237

Query: 226 GQQLLNDPKVRAAYLGE 242
            +Q+ ++P+V  AYLGE
Sbjct: 238 PEQIRDNPEVIKAYLGE 254


Lambda     K      H
   0.317    0.136    0.373 

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: 128
Number of extensions: 6
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: 242
Length of database: 255
Length adjustment: 24
Effective length of query: 218
Effective length of database: 231
Effective search space:    50358
Effective search space used:    50358
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: 41 (21.7 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