GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctO in Dinoroseobacter shibae DFL-12

Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate 3607536 Dshi_0948 L-lactate dehydrogenase (cytochrome) (RefSeq)

Query= BRENDA::Q8Z0C8
         (365 letters)



>FitnessBrowser__Dino:3607536
          Length = 390

 Score =  238 bits (608), Expect = 2e-67
 Identities = 140/372 (37%), Positives = 217/372 (58%), Gaps = 24/372 (6%)

Query: 12  EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71
           + +++ K  + +M +DY  SG+  E T +EN + F+ +KLR R+ +D+   +  T+++GQ
Sbjct: 9   DLKRIYKRRVPKMFYDYAESGSWTEQTFRENSSDFDLLKLRQRIAMDMDNRSTKTTMVGQ 68

Query: 72  PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131
            + +P+ +AP+    + H +GE+  A AA   G    LST+S  S+E+VA      + + 
Sbjct: 69  EVAMPVALAPVGLTGMQHADGEIKAARAAEKFGVPFTLSTMSICSIEDVAA----HTETP 124

Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGL---HL 188
            WFQ+Y  KD    + L +RA  A   AL +TVD  +LGQR RD +N    PP L    +
Sbjct: 125 FWFQVYTLKDDDFMKRLFDRAKEAKCSALVITVDLQLLGQRHRDLKNGLSAPPKLTPASI 184

Query: 189 ANLTT--------------ISGLNIPHAPG---ESGLFTYFAQQLNPALTWDDLEWLQSL 231
           AN+ T                G  + HA G    S L ++ A+  + +L W+ ++  +S 
Sbjct: 185 ANMMTKVQWGLGMLGTKRRFFGNIVGHAKGVTDPSSLSSWTAEAFDQSLDWERIKQFRSW 244

Query: 232 SPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEV 291
              P++LKGIL  +DA  A+  GA AIV SNHGGRQLDGA++S+  LP+I+ AV  K EV
Sbjct: 245 WDGPVILKGILDPEDAKMALNVGADAIVCSNHGGRQLDGALSSIRMLPQIMDAVGDKIEV 304

Query: 292 LLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIG 351
            LD GIR G D++KA+A+GA+  +IGR   +GL   G+AGV+  + ++ KEL+++M L G
Sbjct: 305 HLDSGIRSGQDVLKAVALGARGTMIGRAWTYGLGAMGEAGVTRALEVIHKELDLSMGLCG 364

Query: 352 CSQLQDIDTSFL 363
              ++D+D S L
Sbjct: 365 RRSVEDLDASNL 376


Lambda     K      H
   0.320    0.136    0.391 

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: 309
Number of extensions: 15
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: 365
Length of database: 390
Length adjustment: 30
Effective length of query: 335
Effective length of database: 360
Effective search space:   120600
Effective search space used:   120600
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: 50 (23.9 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