GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Magnetospirillum magneticum AMB-1

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_043743254.1 AMB_RS02640 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_000009985.1:WP_043743254.1
          Length = 415

 Score =  356 bits (913), Expect = e-102
 Identities = 189/391 (48%), Positives = 258/391 (65%), Gaps = 3/391 (0%)

Query: 5   TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64
           TI  +D++GKRV++R D NVP KDG V D TRI  +  T+     +GAKVI+L+H GRPK
Sbjct: 4   TIDKLDVQGKRVLVRADLNVPAKDGKVTDTTRIDRSAATLIQLAAKGAKVIVLTHFGRPK 63

Query: 65  GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124
           G    ++S   + + L++ +GK V +    +G +V+K +  +K+G++ LLEN RFHP E 
Sbjct: 64  GRED-KYSQKLLVEPLAKAVGKAVAWADDCIGPDVEKLIASMKDGDIALLENVRFHPEEE 122

Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYN 184
           KNDP  AK  A+L D +VNDAF TAHRAHAS  G+A  +P+ AG LM+ E++ L K    
Sbjct: 123 KNDPAFAKALAALGDAYVNDAFSTAHRAHASTEGLAHLLPAAAGRLMQAELEALGKALEA 182

Query: 185 PEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKID 244
           PEKP   ++GGAKVS K+ ++ NL+ K D ++IGG M  TFL A GK+VG S  E+D  D
Sbjct: 183 PEKPVAAIVGGAKVSTKLDLLGNLVSKVDYLIIGGGMANTFLFAQGKQVGKSLCEKDLAD 242

Query: 245 LAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELF 304
            A+ +LEKAKE    IVLPVDAV+A +       +VV + D +P   M LD GP + E  
Sbjct: 243 TARAILEKAKEAKCHIVLPVDAVVAGEFAENAANEVVSV-DAVPADKMILDAGPASAEAI 301

Query: 305 KQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKG-AITVVGGGDSAAAVNKF 363
             +L   KT+VWNGP+G FEI  F + T  VA   A  T +G  +TV GGGD+ +A+ K 
Sbjct: 302 IDRLGGCKTLVWNGPLGAFEIAPFDKATNAVAQWAAERTLQGKLLTVGGGGDTVSALAKA 361

Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
           G+E+KFS++ST GGA LE+LEGKELPG+A++
Sbjct: 362 GVEEKFSYISTAGGAFLEWLEGKELPGVAAL 392


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: 674
Number of extensions: 30
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: 415
Length adjustment: 35
Effective length of query: 619
Effective length of database: 380
Effective search space:   235220
Effective search space used:   235220
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