GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Sphingopyxis indica DS15

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_089214652.1 CHB69_RS04180 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_900188185.1:WP_089214652.1
          Length = 398

 Score =  343 bits (881), Expect = 6e-99
 Identities = 183/392 (46%), Positives = 246/392 (62%), Gaps = 3/392 (0%)

Query: 5   TIRDV-DLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63
           T+ D+ D+ GKRV++RVD NVP+ DG V D TR++AA+PTI+   ++GA V+LL+H GRP
Sbjct: 6   TLDDIGDVTGKRVLVRVDLNVPMADGAVSDATRLQAAVPTIRELSDKGAIVLLLAHFGRP 65

Query: 64  KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123
           KG  +P  SL+ V   L ++LG  V F+P  +GD  K  V  L  G+V +LENTRF+PGE
Sbjct: 66  KGAKNPAQSLSLVMGGLEDVLGHSVMFIPDCIGDGAKAGVAVLAPGDVAVLENTRFYPGE 125

Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTY 183
            KNDP  A   A + D++VNDAF  AHRAH S  GIA  +P+ AG  ME E+K L     
Sbjct: 126 EKNDPAFADALAEIGDLYVNDAFSAAHRAHGSTEGIAHRLPAFAGRAMEAELKALDAALG 185

Query: 184 NPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKI 243
           NP  P   V+GGAKVS KI V+ NL+ + D ++IGG M  TFL A G +VG S  E D +
Sbjct: 186 NPAHPVAAVVGGAKVSTKIDVLKNLVGRVDHLIIGGGMANTFLAARGVDVGKSLCEHDLV 245

Query: 244 DLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIEL 303
           D A  + E A   G  I LP D V+A++  P    + V + +  P+  M LD+GP  +E 
Sbjct: 246 DTANAIFEAADSAGCTIHLPYDVVVAREFAPNPPTRTVNVHEVAPDE-MILDVGPAAVEA 304

Query: 304 FKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGA-ITVVGGGDSAAAVNK 362
               L   +T+VWNGP+G FE   F   T  +A   AALT +G+ I+V GGGD+ AA+N 
Sbjct: 305 LADVLKTCRTLVWNGPLGAFETPPFDAATVALAKTAAALTREGSLISVAGGGDTVAALNH 364

Query: 363 FGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394
            G+   F+ VST GGA LE++EGK LPG+ ++
Sbjct: 365 AGVAGDFTFVSTAGGAFLEWMEGKPLPGVDAL 396


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: 619
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 24 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