GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Dinoroseobacter shibae DFL-12

Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate 3609492 Dshi_2876 malate dehydrogenase, NAD-dependent (RefSeq)

Query= BRENDA::Q8I8U5
         (330 letters)



>FitnessBrowser__Dino:3609492
          Length = 320

 Score =  326 bits (836), Expect = 4e-94
 Identities = 160/321 (49%), Positives = 227/321 (70%), Gaps = 5/321 (1%)

Query: 9   RPKIAMVGSGMIGGTMAFLCSLRELGDVVLFDVVPNMPMGKAMDISHNSSVVDTGITVYG 68
           RPKIA++G+G IGGT+A L +L+ELGDVVLFD+    P GKA+DI+ +  V     ++ G
Sbjct: 3   RPKIALIGAGQIGGTLAHLVALKELGDVVLFDIADGTPQGKALDIAESGPVERFDASLKG 62

Query: 69  SNSYECLKGADVVIITAGITKIPGKSDKEWSRMDLLPVNIKIMREVGAAIKSYCPNAFVI 128
           +  Y  + GADV I+TAG+ + PG S     R DLL +N+K+M+ VG  I +  P+AFVI
Sbjct: 63  TTDYADIAGADVCIVTAGVPRKPGMS-----RDDLLGINLKVMKSVGEGIAANAPDAFVI 117

Query: 129 NITNPLDVMVAALQESSGLPHHRICGMAGMLDSSRFRRMIADKLEVSPRDVQGMVIGVHG 188
            ITNPLD MV ALQ+ SGLP  ++ GMAG+LDS+RFR  +A++  VS +DV   V+G HG
Sbjct: 118 CITNPLDAMVWALQQFSGLPKEKVVGMAGVLDSARFRHFLAEEFNVSMKDVTAFVLGGHG 177

Query: 189 DHMVPLSRYATVNGIPLSEFVKKGWIKQEEVDDIVQKTKVAGGEIVRLLGQGSAYYAPGA 248
           D MVPL+RY+TV GIPL + V+ GW  QE++D IVQ+T+  G EIV LL  GSA+YAP A
Sbjct: 178 DTMVPLTRYSTVAGIPLPDLVEMGWTSQEKLDAIVQRTRDGGAEIVGLLKTGSAFYAPAA 237

Query: 249 SAIQMAESYLKDRKRVMVCSCYLQGQYGVQNHYLGVPCVIGGRGVEKIIELELTAQERQE 308
           SA++MAE+YLKD+KR++ C+ Y  G++G+ + Y+GVP +IG  G+EK+++++L   E+  
Sbjct: 238 SAVEMAEAYLKDQKRLLPCAAYCDGEFGLNDMYVGVPTIIGAGGIEKVVDIKLGKDEQAM 297

Query: 309 LQGSIDEVKEMQKAIAALDAS 329
              S++ VK + +A   +D S
Sbjct: 298 FDNSVNAVKGLMEACKGIDDS 318


Lambda     K      H
   0.319    0.136    0.394 

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: 333
Number of extensions: 16
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: 330
Length of database: 320
Length adjustment: 28
Effective length of query: 302
Effective length of database: 292
Effective search space:    88184
Effective search space used:    88184
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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