GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Desulfacinum hydrothermale DSM 13146

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_084057910.1 B9A12_RS10820 D-glycerate dehydrogenase

Query= BRENDA::O66939
         (334 letters)



>NCBI__GCF_900176285.1:WP_084057910.1
          Length = 330

 Score =  166 bits (421), Expect = 6e-46
 Identities = 112/327 (34%), Positives = 175/327 (53%), Gaps = 24/327 (7%)

Query: 1   MNVLFTS-VPQEDVPFYQEALKDLSLKIYTTDVSKVPE-NELKKAELISVFVYDKLTEEL 58
           M VL T+ +P+  V   +EA  ++ + ++   + +    N ++    +   + D++  E+
Sbjct: 1   MKVLVTARLPEAVVGKIREAGHEVDMHLHMAPLERDQLLNRMEGVAGLLSTITDRIDGEV 60

Query: 59  LSKMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSPESVAEHTFAMILTLVKRLKR 118
             + P L+++    VGFDHID+    ++GILVT+ P    ++ A+ TFA+IL + +R+  
Sbjct: 61  FDRAPGLRVVANYGVGFDHIDVAEATRRGILVTNTPGVLTDATADLTFALILAVARRVVE 120

Query: 119 IEDRVK--KLNFSQDSEILARELNRLTLGVIGTGRIGSRVAMYGLAFGMKVLCYDVVK-- 174
            + R +  K  F      L  E++  TLG++G GRIG  VA     F M+VL Y   K  
Sbjct: 121 GDHRTRSGKFQFWAPLHFLGTEVSGKTLGIVGLGRIGRAVARRARGFDMQVL-YTARKPL 179

Query: 175 -REDLKEKGCVYTSLDELLKESDVISLHVPYTKETHHMINEERISLMKDGVYLINTARGK 233
            R++ +  G  +  LD+LL  SD +SLHVP T ETHH+I    +SLMK   YLINTARG 
Sbjct: 180 GRDEEERLGVRFAPLDQLLARSDFVSLHVPLTPETHHLIGARELSLMKPFAYLINTARGP 239

Query: 234 VVDTDALYRAYQRGKFSGLGLDVFEDEEILILKKYTEGKATDKNLKILELACKDNVIITP 293
           VVD  AL  A ++ +  G GLDV+E+E  L     T G           LA   NV++ P
Sbjct: 240 VVDETALLEALRQRRIGGAGLDVYENEPQL-----TPG-----------LADLQNVVLLP 283

Query: 294 HIAYYTDKSLERIREETVKVVKAFVKG 320
           H+   T ++  R+ +  V+ + A + G
Sbjct: 284 HVGSATVETRTRMAQMAVENLLAGLSG 310


Lambda     K      H
   0.319    0.138    0.383 

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: 250
Number of extensions: 16
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: 334
Length of database: 330
Length adjustment: 28
Effective length of query: 306
Effective length of database: 302
Effective search space:    92412
Effective search space used:    92412
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 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