GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Synechococcus elongatus PCC 7942

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Synpcc7942_1116 Synpcc7942_1116 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__SynE:Synpcc7942_1116
          Length = 402

 Score =  455 bits (1171), Expect = e-132
 Identities = 226/389 (58%), Positives = 290/389 (74%), Gaps = 3/389 (0%)

Query: 10  DLKGKRVIMRVDFNVPVK-DGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPS 68
           DL+GKRV++RVDFNVP+  +G + DDTRIRAALPTI+Y  E GAKVIL+SH GRPKG+P 
Sbjct: 13  DLEGKRVLVRVDFNVPLDGNGKITDDTRIRAALPTIRYLSESGAKVILVSHFGRPKGKPV 72

Query: 69  PEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDP 128
               L PVA+RLSELLG+ V      VG   +  V     G+V+LLEN RFH  E  ND 
Sbjct: 73  ESMRLTPVAERLSELLGRPVVKTTDAVGAGAEAQVAATSNGQVVLLENVRFHAEEEANDA 132

Query: 129 ELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFI-PSVAGFLMEKEIKFLSKVTYNPEK 187
           E AK  ASLADI+VNDAFG AHRAHAS  G+ +++ P VAG+L+EKE+++L     NP++
Sbjct: 133 EFAKALASLADIYVNDAFGAAHRAHASTAGVTEYLSPCVAGYLLEKELQYLQAAIDNPQR 192

Query: 188 PYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAK 247
           P   ++GG+KVS KIGVI  L++K D++LIGG M+FTF KA G  VG S VEEDK+DLA+
Sbjct: 193 PLAAIVGGSKVSSKIGVIETLLDKCDKLLIGGGMIFTFYKAQGLSVGGSLVEEDKLDLAR 252

Query: 248 ELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQK 307
            L+ KA+EKGV+++LPVD V+A K  P    K V ID  IP+GWMGLDIGPE+++ F++ 
Sbjct: 253 SLMAKAQEKGVQLLLPVDVVVADKFAPDANAKTVAID-AIPDGWMGLDIGPESVKQFEEA 311

Query: 308 LSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGLED 367
           L+D ++V+WNGPMGVFE D FA GT+ +A ++A LT KGA T++GGGDS AAV K G+  
Sbjct: 312 LADCRSVIWNGPMGVFEFDQFAVGTEAIARSLAGLTRKGATTIIGGGDSVAAVEKVGVAS 371

Query: 368 KFSHVSTGGGASLEFLEGKELPGIASIAD 396
           + SH+STGGGASLE LEGK LPG+A++ D
Sbjct: 372 EMSHISTGGGASLELLEGKVLPGVAALDD 400


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: 702
Number of extensions: 34
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: 402
Length adjustment: 35
Effective length of query: 619
Effective length of database: 367
Effective search space:   227173
Effective search space used:   227173
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