GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Tistlia consotensis USBA 355

Align D-mannonate dehydratase Caul1835; ManD; EC 4.2.1.8 (characterized)
to candidate WP_085125981.1 B9O00_RS27750 mandelate racemase/muconate lactonizing enzyme family protein

Query= SwissProt::B0T4L2
         (403 letters)



>NCBI__GCF_900177295.1:WP_085125981.1
          Length = 400

 Score =  155 bits (393), Expect = 2e-42
 Identities = 120/400 (30%), Positives = 187/400 (46%), Gaps = 44/400 (11%)

Query: 15  GRNFVTLKIETSDGVYGVGDA-TLNGRELPVVSYLTDHVIPCLIGRDAHRIEDIWQYLYK 73
           GR FV +K+ T  GV G+G+   L      VV+ + D     L+G+D  RIE +W+ +Y 
Sbjct: 20  GRYFVFVKLVTDGGVEGLGEVYCLPFHPRVVVAMIEDLAGRYLVGQDPTRIESLWRRVYS 79

Query: 74  GAYWRRGPVTMAAI-AAVDMALWDIKAKIAGLPLYQLLGGACREGIMVYGH---ANGATI 129
             Y +R  +++A I + ++MA WDI  K  G P++ LLGG   E +  Y +     G T 
Sbjct: 80  AGYGQRPDLSVAGILSGLEMACWDILGKETGKPVHALLGGRVHERLRSYTYLYPGEGETA 139

Query: 130 ------EETLENAAVYAAQGYKAIRLQSGVPGLKGVYGVSKDKFFYEPADGDLPT-ESLW 182
                 E + E AA Y  QG+ AI+     P              Y   D  +P  ESL 
Sbjct: 140 DFYHDAERSAERAAEYVRQGFTAIKFDPAGP--------------YSAFDPRMPDQESLA 185

Query: 183 STEKYLRSAPGLFEAARDKLGWDLHLLHDVHHRLTPIEAGRLGKDLEPYRPFWMEDAVPA 242
            +E++ R    L  AA   +G    LL   H + TP  A RL + LEPY P W+E+  P 
Sbjct: 186 RSEQFCR----LIRAA---VGGGADLLFGTHGQFTPAGALRLARRLEPYDPLWLEEPTPP 238

Query: 243 ENQASFRLIRQHTTTPLAVGEVFNSIWDCKQLIEEQLIDYIRATVVHAGGITHLRKIASF 302
           E      L+ + TT P+A GE   + ++  +L++      ++  +   GG+   +KIA  
Sbjct: 239 EMPEQMALVARGTTIPVAAGERLATKYEFARLLDAGAAAILQPNLGRVGGLLEAKKIAGL 298

Query: 303 ADLHHVRTGCHGATDLSPIAMAAALHFDLSIPNFGIQEYMR-----HTEATDTVFPHAYT 357
           A+  + +   H      P+  AA +    ++PNF I E ++     H E   T       
Sbjct: 299 AEARYAQVAPH--LYCGPVVGAANIQLAATLPNFLILESIQTWGGFHAELLKT----PIR 352

Query: 358 FNDGMLHPGDAVGLGVDINETEAAKYPYKRAYLPIARRED 397
           + +G +   DA GLGV+++E  A  +PY+   L +   +D
Sbjct: 353 WQEGYVLVPDAPGLGVELDEAVALAHPYEGEELHLDMAQD 392


Lambda     K      H
   0.321    0.138    0.434 

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: 414
Number of extensions: 21
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: 403
Length of database: 400
Length adjustment: 31
Effective length of query: 372
Effective length of database: 369
Effective search space:   137268
Effective search space used:   137268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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