GapMind for catabolism of small carbon sources

 

Alignments for a candidate for QDPR in Marinobacter adhaerens HP15

Align dihydromonapterin reductase (EC 1.5.1.50) (characterized)
to candidate GFF3777 HP15_3719 short-chain dehydrogenase/reductase SDR

Query= BRENDA::P0AFS3
         (240 letters)



>FitnessBrowser__Marino:GFF3777
          Length = 235

 Score =  251 bits (640), Expect = 1e-71
 Identities = 129/232 (55%), Positives = 164/232 (70%), Gaps = 1/232 (0%)

Query: 8   PILITGGGRRIGLALAWHFINQKQPVIVSYRTHYPAIDGLINAGAQCIQADFSTNDGVMA 67
           PILITG G+RIGLA A   +++ QP+IV+YRT+ PAID L  AGA C+ ADF+TN G+  
Sbjct: 4   PILITGAGQRIGLAFARACLDRGQPIIVTYRTYRPAIDALQKAGAVCLHADFATNAGIDD 63

Query: 68  FADEVLKSTHGLRAILHNASAWMAEKPGAPLADVLACMMQIHVNTPYLLNHALERLLRGH 127
           F   +   T  LRAI+HNAS W+ E   +  ADV+  MMQIHV TPY +N     +L   
Sbjct: 64  FIQALKSRTDTLRAIIHNASDWIPESEDSDPADVMNAMMQIHVMTPYRINLTCRSMLEQE 123

Query: 128 GHAASDIIHFTDYVVERGSDKHIAYAASKAALDNMTRSFARKLAPEVKVNSIAPSLILFN 187
           G + +DIIH TDYVVE+GS KHIAYAASKAAL N+T SFAR LAP VKVN++APSLI+FN
Sbjct: 124 G-STTDIIHMTDYVVEKGSAKHIAYAASKAALTNLTLSFARLLAPRVKVNAVAPSLIMFN 182

Query: 188 EHDDAEYRQQALNKSLMKTAPGEKEVIDLVDYLLTSCFVTGRSFPLDGGRHL 239
           + D   YR++ L KSLM   PG +  +  + +LL + ++TGR+ PLDGGRHL
Sbjct: 183 QGDSQAYREKTLKKSLMGIEPGAEVAVATLQFLLDNPYITGRTLPLDGGRHL 234


Lambda     K      H
   0.322    0.136    0.407 

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: 186
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: 240
Length of database: 235
Length adjustment: 23
Effective length of query: 217
Effective length of database: 212
Effective search space:    46004
Effective search space used:    46004
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 (21.9 bits)
S2: 46 (22.3 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