GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Brucella inopinata BO1

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_008507384.1 BIBO1_RS12005 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_000182725.1:WP_008507384.1
          Length = 396

 Score =  338 bits (867), Expect = 3e-97
 Identities = 180/388 (46%), Positives = 250/388 (64%), Gaps = 2/388 (0%)

Query: 5   TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64
           T+ D +++ +RV++RVD NVP+ +G V D TRI   +PTI     +GAKVILL+H GRPK
Sbjct: 5   TLDDANVQSRRVLVRVDLNVPMANGEVTDLTRIERIVPTIAELSRKGAKVILLAHFGRPK 64

Query: 65  GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124
           G  S E SL  V K LS++L   V F    +GD+ K AV+ LK+G+VLLLENTRFH GE 
Sbjct: 65  GVASDENSLKHVVKPLSKVLDHGVHFAEDCIGDKAKAAVDALKDGDVLLLENTRFHKGEE 124

Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYN 184
           KNDPE  +  A   D++VNDAF  AHRAHAS  G+A  +P+ AG  M+ E++ L K   N
Sbjct: 125 KNDPEFVQALAVNGDLYVNDAFSAAHRAHASTEGLAHVLPAFAGRAMQAELEALEKGLGN 184

Query: 185 PEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKID 244
           P +P V ++GGAKVS K+ +++NL+EK D ++IGG M  TFL A G +VG S  E +   
Sbjct: 185 PARPVVAIVGGAKVSTKLDLLSNLIEKVDALVIGGGMANTFLAAKGLDVGKSLCEHELAS 244

Query: 245 LAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELF 304
            A+E++ KA+     I+LPVDAV+          +   + D +P   M LD G  + +L 
Sbjct: 245 TAREIMAKAETTKCAIILPVDAVVGWHFAADTPHQTYGV-DSVPGDAMILDAGELSTDLI 303

Query: 305 KQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKG-AITVVGGGDSAAAVNKF 363
              + DA T+VWNGP+G FE+  F   T +VA  +A  T++G  ++V GGGD+ AA+N  
Sbjct: 304 ASAIDDAATLVWNGPLGAFELRPFDTATVKVARHVAKRTKEGKLVSVGGGGDTVAALNHA 363

Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGI 391
           G+ D F+++ST GGA LE++EGK LPG+
Sbjct: 364 GVADDFTYISTAGGAFLEWMEGKPLPGV 391


Lambda     K      H
   0.317    0.137    0.386 

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: 569
Number of extensions: 21
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: 654
Length of database: 396
Length adjustment: 34
Effective length of query: 620
Effective length of database: 362
Effective search space:   224440
Effective search space used:   224440
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 (21.6 bits)
S2: 52 (24.6 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