GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Dinoroseobacter shibae DFL-12

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 3608763 Dshi_2155 Phosphoglycerate kinase (RefSeq)

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__Dino:3608763
          Length = 393

 Score =  350 bits (899), Expect = e-101
 Identities = 188/391 (48%), Positives = 252/391 (64%), Gaps = 6/391 (1%)

Query: 5   TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64
           T+ D+ L GK V+ RVD NVPV DGVV D TRI   +PT+   L +G   +LL+H GRPK
Sbjct: 5   TLDDMALDGKIVLTRVDINVPVADGVVTDTTRIERIVPTVTDILAKGGLPVLLAHFGRPK 64

Query: 65  GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124
           G+  PE SL  V   L E LG+ V+F+        + A+E L +  V+L ENTRF PGE 
Sbjct: 65  GKVVPEMSLRVVLPALEEALGRPVEFI----AHPDRAALEALPKCTVVLAENTRFAPGEE 120

Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYN 184
           KNDPE+A   A+L DI+ NDAF  AHRAHAS  GIA+ +PS AG LM+ E++ L +    
Sbjct: 121 KNDPEMAAALAALGDIYCNDAFSAAHRAHASTEGIARLLPSCAGRLMQAELEALQRALGT 180

Query: 185 PEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKID 244
           P +P V V+GGAKVS K+ ++ NL+EK D ++IGG M  TFL A G +VG+S  E +  D
Sbjct: 181 PTRPVVAVVGGAKVSTKLALLGNLVEKVDDLVIGGGMANTFLAAQGIDVGASLAEHEMAD 240

Query: 245 LAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELF 304
            A+E++EKA   G  I LP D V+A+K E G   + + + +  P   M LD GPET+   
Sbjct: 241 TAREIMEKAARAGCSIHLPKDIVVARKFEAGAPSQTLPVSE-CPRDAMILDAGPETVAAL 299

Query: 305 KQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGA-ITVVGGGDSAAAVNKF 363
           K+  + A+T++WNGP+G FEI  F   T   A A A  T+ G  ITV GGGD+ AA+NK 
Sbjct: 300 KEVFAQARTLIWNGPLGAFEIPPFDMATNAAARAAADATKAGTLITVAGGGDTVAALNKA 359

Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
           G+ D F+++ST GGA LE++EGK LPG+A++
Sbjct: 360 GVADDFTYISTAGGAFLEWMEGKTLPGVAAL 390


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: 606
Number of extensions: 27
Number of successful extensions: 4
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: 393
Length adjustment: 34
Effective length of query: 620
Effective length of database: 359
Effective search space:   222580
Effective search space used:   222580
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