GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruH in Limnohabitans curvus MWH-C5

Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_108360051.1 B9Z44_RS01960 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::Q9HUI9
         (393 letters)



>NCBI__GCF_003063475.1:WP_108360051.1
          Length = 394

 Score =  154 bits (389), Expect = 4e-42
 Identities = 105/331 (31%), Positives = 163/331 (49%), Gaps = 10/331 (3%)

Query: 34  ILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVDAE 93
           ++ L++G+PDF  P  + +AA  ++  G T Y    G   LR+RI+  +  R G  V A 
Sbjct: 36  MIFLNIGEPDFTAPPLVQEAAARAVHDGVTQYTPALGIPELRERISAWYSTRFGVNVPAR 95

Query: 94  QVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENGFRV 153
           ++V+ AGA  AL      L+  GDEV++ +P Y        A   R V VP  +   F++
Sbjct: 96  RIVITAGASAALQLACLALIEAGDEVLMPDPSYPCNRHFVSAAEGRAVLVPTTAAERFQL 155

Query: 154 QAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELLFD 213
            AE+V A  T +TR + L SP NP+G S+      A+           + DE+Y  L +D
Sbjct: 156 SAEQVRANWTAQTRGVLLASPSNPTGTSIHPDELRAIHNEVSQRGGTTLIDEIYLGLSYD 215

Query: 214 GEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGSPEF 273
            E    ++L G+ D+  ++NS SK   MTGWR+GW+V P AL   +E LA  +   +   
Sbjct: 216 -EQFGQSAL-GLDDQIISINSFSKYFNMTGWRLGWLVVPDALVPVVERLAQNLFICASTV 273

Query: 274 IQDAACTALEA-PLPELEAMREAYRRRRDLVIECLADSPGLR-PLRPDGGMFVMVDIRPT 331
            Q AA    EA  + E E  R  ++ RRD  +  L ++ GL  P+ PDG  +   D    
Sbjct: 274 AQHAALACFEAESMAEYERRRAEFKARRDYFVPAL-NALGLNVPVMPDGAFYAWADCTQA 332

Query: 332 G-----LSAQAFADRLLDRHGVSVLAGEAFG 357
                   +  FA  ++++  +++  G  FG
Sbjct: 333 ANKLGVKGSWDFAFEVMNKANLAITPGRDFG 363


Lambda     K      H
   0.322    0.136    0.411 

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: 370
Number of extensions: 18
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: 393
Length of database: 394
Length adjustment: 31
Effective length of query: 362
Effective length of database: 363
Effective search space:   131406
Effective search space used:   131406
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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