GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alr in Desulfoscipio geothermicus DSM 3669

Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate WP_092483985.1 BM299_RS11030 alanine racemase

Query= SwissProt::Q88GJ9
         (409 letters)



>NCBI__GCF_900115975.1:WP_092483985.1
          Length = 380

 Score =  191 bits (484), Expect = 4e-53
 Identities = 126/366 (34%), Positives = 189/366 (51%), Gaps = 12/366 (3%)

Query: 41  NSNAWVEVSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAV 100
           N+  W E++ +A+ HNIR L+      ++L AV+KA+AYGHG G V    +  G   + V
Sbjct: 4   NTPVWSEINLAAIAHNIRQLKNITRPDAELMAVVKANAYGHGAGQVARVAMENGATRLGV 63

Query: 101 ASNEEARVVRASGFTGQLVRVRLASLSELEDGLQYDMEELVGSAEFARQADAIAARHGKT 160
           A   E   +R +G    L+ +      +    L  D+ + V S   AR+  A AAR GK 
Sbjct: 64  ARVSEGEALRRAGIDAPLLILGYTVPEDYPSLLANDLAQTVYSLAAARELSATAARAGKK 123

Query: 161 LRIHMALNSSGMSRNGV---EMATWSGRGEALQITDQKHLKLVALMTHFAVEDKDDVRKG 217
             +H+ +++ GM R G    + A      E   I    HL++  + THFA  D  D    
Sbjct: 124 AVVHIKVDT-GMGRLGFCIDKEAVKEAVREITAIAKLPHLEVEGIYTHFAAADSRDKSYT 182

Query: 218 LAAFNEQTDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFG-----DTVP 272
           +  + +  + L   +R   + L  HAANS A +++PE  LD+VR G A++G     + + 
Sbjct: 183 IKQWRKFNELLEALSREGLAFLYRHAANSAALIDLPETHLDLVRAGIAIYGVYPSNEVLT 242

Query: 273 ARTEYKRAMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTNKG 332
            R   K AM  K+ VA V   PAG  + Y  T    +D+ +A I  GY+DGY R+ +++G
Sbjct: 243 ERVSLKPAMAVKARVAHVKRVPAGTGISYGVTHITPKDTLVATIPAGYADGYSRLLSSRG 302

Query: 333 HVLINGHRVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFGKQAGGEITQAEMEEINGALL 392
            VL+ G R PV+G+V M+  MVDV    DV+ G EVVL G+Q G ++  A  +EI G + 
Sbjct: 303 EVLLRGRRAPVIGRVCMDQFMVDVGHLSDVEPGEEVVLMGRQ-GDDMVSA--DEIAGKIG 359

Query: 393 ADLYTV 398
              Y V
Sbjct: 360 TIAYEV 365


Lambda     K      H
   0.318    0.132    0.377 

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: 321
Number of extensions: 18
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: 409
Length of database: 380
Length adjustment: 31
Effective length of query: 378
Effective length of database: 349
Effective search space:   131922
Effective search space used:   131922
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 (21.7 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