GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Azospirillum brasilense Sp245

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate AZOBR_RS03885 AZOBR_RS03885 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__azobra:AZOBR_RS03885
          Length = 398

 Score =  362 bits (930), Expect = e-104
 Identities = 186/394 (47%), Positives = 262/394 (66%), Gaps = 2/394 (0%)

Query: 5   TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64
           TI D+D+ GK V++R D NVP++DG V D TRI    PT+    ++GAKV++LSH GRPK
Sbjct: 6   TIDDLDVNGKTVLVRADLNVPMQDGKVSDTTRIDRLAPTLTELAKKGAKVVVLSHFGRPK 65

Query: 65  GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124
             P  + SL  V   LS  +G+ V F    VGD+ K A++ ++ G ++LLENTRFH  E 
Sbjct: 66  NGPDAKNSLRNVLDALSAAVGQTVAFGEDCVGDKAKAAIDGVQPGAIVLLENTRFHAEEE 125

Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYN 184
           KNDP  AK  A+L D++VNDAF  AHRAHAS  G+AQ++P+ AG LM+ E++ L+K    
Sbjct: 126 KNDPAFAKQIAALGDLYVNDAFSAAHRAHASTEGVAQYLPAAAGRLMQAELEALTKALEK 185

Query: 185 PEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKID 244
           PE+P   V+GGAK+S K+ ++ NL++K D + +GG M  TFL A G +VG+S  E+D  D
Sbjct: 186 PERPVAAVVGGAKISTKLDLLGNLVKKVDMLALGGGMANTFLYAQGVDVGASLCEKDMAD 245

Query: 245 LAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELF 304
            A+ ++E AK    E++LP D ++A++ + G   + V   DGI    M LD+GP+T+E  
Sbjct: 246 QARAIMETAKAANCELLLPKDFIVAKEFKAGAANRAVPA-DGIGADEMALDVGPKTVEFL 304

Query: 305 KQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALT-EKGAITVVGGGDSAAAVNKF 363
             KL  AKTVVWNGP+G FEI  F  GT  VA  +A  T E G ++V GGGD+ +A+   
Sbjct: 305 GLKLQGAKTVVWNGPLGAFEIQPFDAGTNAVAGLVAERTSEGGLLSVAGGGDTVSALAHA 364

Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGIASIADK 397
           G+E+KF+++S  GGA LE+LEGK+LPG+A++  K
Sbjct: 365 GVEEKFTYISAAGGAFLEWLEGKDLPGVAALKKK 398


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: 624
Number of extensions: 27
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: 398
Length adjustment: 34
Effective length of query: 620
Effective length of database: 364
Effective search space:   225680
Effective search space used:   225680
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 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