GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Sphingomonas koreensis DSMZ 15582

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate Ga0059261_0219 Ga0059261_0219 Lactate dehydrogenase and related dehydrogenases

Query= BRENDA::A0A140N893
         (329 letters)



>FitnessBrowser__Korea:Ga0059261_0219
          Length = 336

 Score =  334 bits (857), Expect = 2e-96
 Identities = 171/329 (51%), Positives = 228/329 (69%), Gaps = 1/329 (0%)

Query: 1   MKLAVYSTKQYDKKYLQQVNESFGFELEFFDFLLTEKTAKTANGCEAVCIFVNDDGSRPV 60
           M++AV+ TK YD+++L + N +   EL F +  L   TA  A GC AVC+FVND     V
Sbjct: 1   MRVAVFGTKGYDRRFLSEANAAHAHELIFLEPRLDLSTAPLAAGCAAVCVFVNDCVDARV 60

Query: 61  LEELKKHGVKYIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTLNRRI 120
           LE L   GV+ +ALRCAGFNNVDL AA+ LG+ VVRVPAY P AVAE  IG+M+ ++R I
Sbjct: 61  LEALAGSGVRLVALRCAGFNNVDLAAAERLGIDVVRVPAYSPHAVAEFTIGLMLAVDRHI 120

Query: 121 HRAYQRTRDANFSLEGLTGFTMYGKTAGVIGTGKIGVAMLRILK-GFGMRLLAFDPYPSA 179
            RA+ R RD NF+L+GL G  ++G+  GVIGTGKIG  + R L+ GFG  +LA D     
Sbjct: 121 PRAWARVRDNNFALDGLIGRNLHGRMVGVIGTGKIGALVARSLRAGFGCDVLASDVVTDP 180

Query: 180 AALELGVEYVDLPTLFSESDVISLHCPLTPENYHLLNEAAFDQMKNGVMIVNTSRGALID 239
               +GV YV   TL  ++++++LHCPLTP   HL++ AA  + + G++IVNTSRGALID
Sbjct: 181 ELERVGVRYVPRATLLEQAEIVTLHCPLTPVTRHLIDAAAISRAREGLLIVNTSRGALID 240

Query: 240 SQAAIEALKNQKIGSLGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTGHQAFL 299
           + A I+ LK++KIG + +DVYE E DLFFED SN+++ DDVF+RL    NVL TGHQAFL
Sbjct: 241 TAALIDGLKSRKIGGVALDVYEQEADLFFEDLSNEIVGDDVFQRLLTFPNVLVTGHQAFL 300

Query: 300 TAEALTSISQTTLQNLSNLEKGETCPNEL 328
           T EALT+I++TTL ++S+ E G    N +
Sbjct: 301 TEEALTAIAETTLASISDAEAGRELANRV 329


Lambda     K      H
   0.320    0.136    0.389 

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: 278
Number of extensions: 6
Number of successful extensions: 2
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: 329
Length of database: 336
Length adjustment: 28
Effective length of query: 301
Effective length of database: 308
Effective search space:    92708
Effective search space used:    92708
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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