GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Arenitalea lutea P7-3-5

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_019388646.1 P735_RS0113840 polysaccharide biosynthesis protein

Query= SwissProt::Q9ZDJ5
         (341 letters)



>NCBI__GCF_000283015.1:WP_019388646.1
          Length = 653

 Score =  138 bits (347), Expect = 5e-37
 Identities = 103/307 (33%), Positives = 157/307 (51%), Gaps = 23/307 (7%)

Query: 2   FVDKTLMITGGTGSFGNAVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNSKLKFY 61
           F  +T+++TG  GS G+ ++ +   SN   D+K + +  + E    D++  L       Y
Sbjct: 290 FRGETVLVTGAAGSIGSELVKQL--SNF--DVKHLILVDQAESALYDVQQDLKRDGKHNY 345

Query: 62  ---IGDVRNYQSIDDAM--HGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAI 116
              + D+R+   ID     H    VFHAAA K VP  E  P EAI  NV G + +   A 
Sbjct: 346 TAIVADIRDGLRIDSIFQTHKPTMVFHAAAYKHVPLMEKAPYEAIKINVNGTKLLADTAS 405

Query: 117 NNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRG 176
              V K + +STDKAV P + MG +K + E        ++   +T    TR+GNV+ S G
Sbjct: 406 RYNVKKFVFVSTDKAVNPTSVMGATKRIAEMYITC---LQKESKTKFITTRFGNVLGSNG 462

Query: 177 SVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFV-QKSPASTI 235
           SVIPLF  QI+ G  LT+T   +TR+ M++ ++  LVL A   G+ G+IF+     +  I
Sbjct: 463 SVIPLFKKQIEAGSSLTLTHKDITRYFMTIPEASQLVLEAGTMGKGGEIFIFDMGESVKI 522

Query: 236 EVLAKALQEIFGSKNA----IRFIGTRHGEKHYESLVSSEDMAKADDLGGYYR--IPMDG 289
             LAK +  + G +      I   G R GEK YE L+++ +    + L  Y++  +    
Sbjct: 523 FDLAKNMIRLSGLRYPEDIDINVTGLRPGEKLYEELLANGE----NTLSTYHKKILISKT 578

Query: 290 RDLNYAK 296
           R+L+YAK
Sbjct: 579 RELDYAK 585


Lambda     K      H
   0.319    0.135    0.373 

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: 473
Number of extensions: 28
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: 341
Length of database: 653
Length adjustment: 33
Effective length of query: 308
Effective length of database: 620
Effective search space:   190960
Effective search space used:   190960
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 (21.8 bits)
S2: 51 (24.3 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