GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Sphingomonas koreensis DSMZ 15582

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Ga0059261_0728 Ga0059261_0728 phosphoglycerate kinase (EC 2.7.2.3)

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__Korea:Ga0059261_0728
          Length = 397

 Score =  311 bits (798), Expect = 3e-89
 Identities = 169/386 (43%), Positives = 243/386 (62%), Gaps = 5/386 (1%)

Query: 10  DLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSP 69
           D+ GKRV++R D NVP+ DG V DDTR+RAA+PT+    ++GA V++L+H GRPK  PSP
Sbjct: 14  DVTGKRVLVREDLNVPMADGHVTDDTRLRAAVPTVSELADKGAIVLVLAHFGRPK-TPSP 72

Query: 70  EFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPE 129
           E S A + +  S++LG+ V+++    GD    A   L+ G++ +LENTRF  GE KNDP+
Sbjct: 73  ELSTAQLVRPFSQVLGRPVRYIDWE-GDIESTAT--LQPGDIAVLENTRFFGGEEKNDPK 129

Query: 130 LAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYNPEKPY 189
           +   +A+L D +VNDAF  AHRAHAS  G+A  +P+ AG  ME E+  L K   NPE P 
Sbjct: 130 VIDRFAALGDFYVNDAFSAAHRAHASTEGLAHRLPAFAGRQMEAELDALDKALGNPEHPV 189

Query: 190 VVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKEL 249
             V+GGAKVS K+ V+ +L+ + D ++IGG M  TFL A G  VG S  E D    A+E+
Sbjct: 190 AAVVGGAKVSTKLDVLKHLVGQVDHLIIGGGMANTFLAARGVNVGKSLCEHDLTGTAEEI 249

Query: 250 LEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKLS 309
            + A++    I LP D V++++               + E  M LD+GP   E     L 
Sbjct: 250 FDAAEKANCTIHLPYDVVVSKEFAANPPSLRTCNVHEVAEDEMILDVGPAASEALADVLK 309

Query: 310 DAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGA-ITVVGGGDSAAAVNKFGLEDK 368
           + +T+VWNGP+G FE   F   T  +A  +AALT++G+ ++V GGGD+ AA+N+ G+  +
Sbjct: 310 NCRTLVWNGPLGAFETKPFDTATMALAHTVAALTKEGSLVSVAGGGDTVAALNQAGVSSE 369

Query: 369 FSHVSTGGGASLEFLEGKELPGIASI 394
            + VST GGA LE++EGK LPG+A++
Sbjct: 370 MTFVSTAGGAFLEWMEGKALPGVAAL 395


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: 577
Number of extensions: 32
Number of successful extensions: 5
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: 397
Length adjustment: 34
Effective length of query: 620
Effective length of database: 363
Effective search space:   225060
Effective search space used:   225060
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