GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Pf1N1B4_5098 Nitrate ABC transporter, ATP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_2560
         (259 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5098
          Length = 263

 Score =  187 bits (474), Expect = 2e-52
 Identities = 108/252 (42%), Positives = 154/252 (61%), Gaps = 12/252 (4%)

Query: 4   VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63
           V +  VS+ F+T KG R QAL  V+  +   +FV+++G SGCGKST+L ++AGL  A  G
Sbjct: 5   VELTQVSKHFDTKKG-RFQALSNVNLSIARGEFVSLIGHSGCGKSTVLNLIAGLLEANGG 63

Query: 64  RVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIR------FGLRERGMPEAQQKERAA 117
            ++ +G  ++GPG ER +VFQ+++L PWLT   N+       FG RE    +A  K R  
Sbjct: 64  GLICNGREIDGPGPERAVVFQNHSLLPWLTCFGNVHLAVEKVFGKREN---KAALKTRTE 120

Query: 118 YFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQEL 177
             +A VGL       P ++SGGM+QR  IARALA +PKILLMDEPFGALD  TR  +Q+ 
Sbjct: 121 AALAMVGLEHAMHKHPSEISGGMKQRVGIARALAMEPKILLMDEPFGALDALTRAHLQDE 180

Query: 178 LLGIWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTE-LAVDLPHPRH-YTIKTS 235
           LL I  A + TV+ VTHD+DEA+ +++R+ + +  P     E L+V L  PR+   +   
Sbjct: 181 LLRIVAATQSTVVMVTHDVDEAVLLSDRIVMMTNGPAATVGEILSVGLAKPRNRLVLAND 240

Query: 236 PEFMDLKARLTE 247
           PE+   +  + E
Sbjct: 241 PEYHRYRTTVLE 252


Lambda     K      H
   0.322    0.136    0.394 

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: 162
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: 259
Length of database: 263
Length adjustment: 25
Effective length of query: 234
Effective length of database: 238
Effective search space:    55692
Effective search space used:    55692
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 (21.9 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