GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alr in Limnohabitans curvus MWH-C5

Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate WP_108403031.1 B9Z44_RS14805 alanine racemase

Query= BRENDA::Q04HB7
         (371 letters)



>NCBI__GCF_003063475.1:WP_108403031.1
          Length = 353

 Score =  125 bits (314), Expect = 2e-33
 Identities = 103/326 (31%), Positives = 165/326 (50%), Gaps = 20/326 (6%)

Query: 16  SSLAYNVQYTKQVSGAKTLWLAVKSNAYGHGLLQVSKIARECGVDGLAVSVLDEGIAIRQ 75
           ++L  N +  +   G K  +  +K+NAYGHG ++ ++   E   D  AV+ L+EG+ +R+
Sbjct: 12  NALLSNYKKLRTFHGGKA-FAVLKANAYGHGAVRCAR-KLEMDADAFAVAFLEEGLELRE 69

Query: 76  AGIDDFILIL-GPIDVKYAPIASKYHFLTTVSSLDWLKSADKILGKEK-LSVNLAVDTGM 133
           AGI   IL+L G  DVK    A+ + F   VS  + L+  ++     + L+V L ++TGM
Sbjct: 70  AGIQKPILLLEGVFDVKELRKAANHGFWVVVSRHEQLEMIEQCSSAMRGLNVWLKLETGM 129

Query: 134 NRIGVRSKKDLKDEIEFLQE--HSDHFSYDGIFTHFASSDNPDDHYFQRQKNRWYELIDG 191
           NR+G+    D     E++     +   +     TH A +D   D +  +Q  +      G
Sbjct: 130 NRLGL----DGSLACEYIARLCATKAVAKVSFMTHLACADVEGDDFSTKQIEKLMNATRG 185

Query: 192 LIMPRYVHVMNSGAAMYHSKELPGCNSIARVGTVVYGVEPSEGVLGPIDKLKPVFELKSA 251
           L     +   NS A +  +K  P  +  AR+G  +YGV P   V G    L+PV ELKS 
Sbjct: 186 LDCE--LSFCNS-AGVLSAKGPP--SDWARLGIAMYGVNP---VPGSSFSLEPVMELKSQ 237

Query: 252 LTFVKKIPAGEGISYGSKFVTSRDTWIGTLPIGYGDGWLAEYQDFQLLIDGQKCRQVGQI 311
           +  VK + AGEG+ YG     SRD+ +G + +GY DG+        +L+DG+  + +G I
Sbjct: 238 IFDVKNVKAGEGVGYGCTVRVSRDSRVGIVALGYADGYPRNAMGCSVLVDGRLTKTLGVI 297

Query: 312 AMDQMMVALP--HEYPIGTEVTLIGK 335
           +MD + V +        G++V L GK
Sbjct: 298 SMDMLAVDITDLENSGQGSQVELWGK 323


Lambda     K      H
   0.319    0.137    0.410 

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: 322
Number of extensions: 13
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: 371
Length of database: 353
Length adjustment: 29
Effective length of query: 342
Effective length of database: 324
Effective search space:   110808
Effective search space used:   110808
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 (21.7 bits)
S2: 49 (23.5 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