GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctO in Dyella japonica UNC79MFTsu3.2

Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate N515DRAFT_1250 N515DRAFT_1250 L-lactate dehydrogenase (cytochrome)

Query= BRENDA::Q8Z0C8
         (365 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1250
          Length = 379

 Score =  279 bits (713), Expect = 1e-79
 Identities = 164/382 (42%), Positives = 228/382 (59%), Gaps = 27/382 (7%)

Query: 4   ISSPI-NLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQI 62
           +++PI N+ +  +LA+  + +  F+Y   GA DE+TL+ NRA  E IK R R++++V Q 
Sbjct: 1   MATPITNVLDLRELARRRVPRAFFEYADRGAYDEVTLRGNRAALESIKFRQRVMMNVDQR 60

Query: 63  NLTTSVLGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAE 122
           +L TSV+GQP+ +PL IAP     L H  GE+  A AA  AG    LST+S  S+E+V +
Sbjct: 61  SLATSVVGQPISMPLAIAPTGLTGLQHGAGEILGARAATKAGIPFCLSTVSICSIEQVRD 120

Query: 123 -VGSKFSPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFV 181
            V + F     WFQLY+ +DRG  R L+ RA  AG  AL LT D  V GQR R+ +N   
Sbjct: 121 AVQAPF-----WFQLYVMRDRGFARDLIRRASDAGCSALMLTADLTVQGQRHREIKNGLS 175

Query: 182 LPPGLHLANLTTISGL-----NIPHAPGES---------------GLFTYFAQQLNPALT 221
           +PP + L NL  +        ++  AP  S                L  + A Q +P L 
Sbjct: 176 VPPKITLRNLFDVMSKPRWAWSMLRAPSRSFGNLAGRIQGTDSLTTLAQWIANQFDPTLN 235

Query: 222 WDDLEWLQSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEI 281
           W DLEW++ L P  L+LKGI+  +DA  A  +G  AIVVSNHGGRQLDGA AS++ LP I
Sbjct: 236 WQDLEWIRELWPGKLILKGIMDEEDARLAAAHGVDAIVVSNHGGRQLDGAPASIEVLPRI 295

Query: 282 VAAVNGKAEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQK 341
             AV  K +VL DGGI  G D++KALA+GA+A LIG+  L+GL   G+ GV+  I ++++
Sbjct: 296 ADAVGDKLDVLFDGGILSGQDVLKALALGARAGLIGKAFLYGLGALGEDGVARTIEIIRR 355

Query: 342 ELNVAMALIGCSQLQDIDTSFL 363
           EL+V+MAL G + ++ I    L
Sbjct: 356 ELSVSMALTGQTDVRRIGRDVL 377


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: 324
Number of extensions: 9
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 365
Length of database: 379
Length adjustment: 30
Effective length of query: 335
Effective length of database: 349
Effective search space:   116915
Effective search space used:   116915
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