GapMind for catabolism of small carbon sources

 

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

Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; N-methyl-L-amino acid dehydrogenase; EC 1.5.1.21; EC 1.4.1.17 (characterized)
to candidate 3609158 Dshi_2546 Malate/L-lactate dehydrogenase (RefSeq)

Query= SwissProt::Q4U331
         (343 letters)



>FitnessBrowser__Dino:3609158
          Length = 351

 Score =  162 bits (411), Expect = 9e-45
 Identities = 119/346 (34%), Positives = 168/346 (48%), Gaps = 14/346 (4%)

Query: 9   PTQTVSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIPGYLSSLAS 68
           P  T+S   L D + R     G   + A+ +A     A   G  +HG+FR+  YL+ L  
Sbjct: 2   PDDTISAEALQDFVARALSARGVPTQDANKVAGLMVEADIYGYGTHGVFRLRQYLARLEG 61

Query: 69  GWVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIRGSHHFA 128
           G  +      V     A   +D  NGF   A+AAAR L ++KAR AG+  + +R  +H  
Sbjct: 62  GGCNPAPNISVLQQTVATALIDGDNGFGHLAMAAARDLAMEKARQAGIGWVGVRRGNHAG 121

Query: 129 ALWPDVEPFAEQGLVALSM-VNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLAT 187
            L   V P AE GL+ ++  V S   V P+G    L GTNPIAF AP  G +P VFD+AT
Sbjct: 122 PLALYVRPQAEAGLLGMAAAVGSANHVPPYGGTDLLLGTNPIAFSAPAEGPDPFVFDMAT 181

Query: 188 SAIAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVEL 247
           +  A G ++   ++G  +P G  V RDG P  +P A    G LLP GG KG  LS+ + L
Sbjct: 182 TVAAMGKIKTLLQQGADMPEGWMVGRDGKPLTDP-ARKSEGFLLPIGGPKGFGLSVAIGL 240

Query: 248 LAAGLTGGNFSFE-FDWSKHPGAQTPWTGQLLIVIDPDK-GAGQHFAQRSEELVRQ---- 301
           +A  L G  F  +  D++    + T  TGQ ++ +DP   G G  FA+ +  +  +    
Sbjct: 241 MAGVLNGAAFGSDVVDFTSDTTSPTN-TGQFVMALDPAAFGLGDGFAETARRVFGEMRAS 299

Query: 302 --LHGVGQERLPGDRRYLERARSMAHGIVIAQA---DLERLQELAG 342
             L G    RLPGD +          G+ +  A   DL+ L E  G
Sbjct: 300 PPLPGHHPVRLPGDGKTQAAETRRRQGLTLNPALRKDLDALAEKYG 345


Lambda     K      H
   0.320    0.137    0.412 

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: 372
Number of extensions: 29
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: 343
Length of database: 351
Length adjustment: 29
Effective length of query: 314
Effective length of database: 322
Effective search space:   101108
Effective search space used:   101108
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.

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