GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alr in Caldicellulosiruptor hydrothermalis 108

Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate WP_013402806.1 CALHY_RS04440 alanine racemase

Query= BRENDA::Q04HB7
         (371 letters)



>NCBI__GCF_000166355.1:WP_013402806.1
          Length = 390

 Score =  167 bits (424), Expect = 3e-46
 Identities = 119/372 (31%), Positives = 201/372 (54%), Gaps = 20/372 (5%)

Query: 12  EFSKSSLAYNVQYTKQVSGAKTLWLAV-KSNAYGHGLLQVSKIARECGVDGLAVSVLDEG 70
           E    +L YN++  K+    +T  +AV K++AYGHG +++S++  + GV  LAV+++DE 
Sbjct: 13  EIDLDNLVYNLENIKKKILPQTHIMAVVKADAYGHGAVEISRVLVKNGVSMLAVAIIDEA 72

Query: 71  IAIRQAGIDDFILILG--PIDVKYAPIASKY-HFLTTVSSLDWLKSADKILGKEKLSVNL 127
           + +R    D  ILILG  P ++    + ++    + T     +L  A + +GK K  +++
Sbjct: 73  LQLRHFNFDVPILILGFTPFELSEQVVENEISQTVYTYEQAYYLSQAAQKVGK-KAKIHI 131

Query: 128 AVDTGMNRIGVRSKKDLKDEIEFLQEHSDHFSYDGIFTHFASSDNPDDHYFQRQK----- 182
            VDTGM RIG     +    +  + +   +   +GIF+HF+S+D+PD   F  ++     
Sbjct: 132 KVDTGMGRIGFLCCDESIQTVLNIAK-LPNIELEGIFSHFSSADDPDSDNFTHEQFMKFE 190

Query: 183 NRWYELIDGLIMPRYVHVMNSGAAM-YHSKELPGCNSIARVGTVVYGVEPSEGVLGPIDK 241
           N   EL    +  +Y H+ NS AA+ +   +L     + R+G ++YG+ P+  +   I  
Sbjct: 191 NFVKELNKNGVYFKYKHIANSSAAIRFPQYQL----DVVRLGLILYGLYPNSSLKEHIS- 245

Query: 242 LKPVFELKSALTFVKKIPAGEGISYGSKFVTSRDTWIGTLPIGYGDGWL-AEYQDFQLLI 300
           +KPV  +K+ +  VK++P G  ISY  +++T+R + I T+PIGY DG+         +LI
Sbjct: 246 IKPVMSVKARVINVKEVPEGFPISYNRRYITTRKSKIATIPIGYADGFTRVGSSQRHVLI 305

Query: 301 DGQKCRQVGQIAMDQMMVALP--HEYPIGTEVTLIGKSGKYENTLYDLHKHSGVPPWKIT 358
            G+  + VG I MDQ MV +    +  IG EV +IGK GK E     L +  G   ++I 
Sbjct: 306 KGEFAKVVGSICMDQCMVDVTDIEDVKIGDEVVIIGKQGKNEILADHLAEQIGTINYEIV 365

Query: 359 VAFSDRLKRMVV 370
            +FS R+ R+ +
Sbjct: 366 CSFSKRIPRVYI 377


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: 345
Number of extensions: 18
Number of successful extensions: 6
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: 390
Length adjustment: 30
Effective length of query: 341
Effective length of database: 360
Effective search space:   122760
Effective search space used:   122760
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: 50 (23.9 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