GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Erythrobacter gangjinensis K7-2

Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate WP_156172064.1 AAW01_RS05295 mannitol dehydrogenase family protein

Query= BRENDA::O08355
         (493 letters)



>NCBI__GCF_001010925.1:WP_156172064.1
          Length = 486

 Score =  306 bits (785), Expect = 8e-88
 Identities = 177/469 (37%), Positives = 257/469 (54%), Gaps = 11/469 (2%)

Query: 13  PEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKA 72
           PE + P Y  A    G+ H+G G FHRAHQA Y DAL++ G    W ICG  LRS     
Sbjct: 4   PEARTPCYDRAQPC-GVLHLGTGAFHRAHQATYFDALLSAGHN-GWMICGASLRSP--AV 59

Query: 73  RDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTIT 132
              +  QD LFT+  + D  + +V ++GS++++++A ++  AL+  LA  ++ +V+LT+T
Sbjct: 60  SRQMNPQDGLFTVL-IRDGGEEQVEIVGSVAEVMVAPENPSALVSALAHSDVALVTLTVT 118

Query: 133 EGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNL 192
           E GYC+D + G        +  D+A  +SP+T  GF+ A L  R+AAGI  FTV+SCDNL
Sbjct: 119 EKGYCLDPATGALNLDDEGVAGDIADIASPQTAPGFLVAGLAARKAAGIAPFTVLSCDNL 178

Query: 193 PHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDD 252
           P NG  TR+A+L  A   +  L  WI+  V+FP +MVDRI P T+           G+ D
Sbjct: 179 PDNGKRTREAVLTLARAVDPALATWIEDEVAFPCSMVDRIVPATTEEDLDNFESATGLRD 238

Query: 253 AWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFL 312
              V  EPF QWV+ED F N RP  ++VGVQ T+DV  +E +K+ LLNG+H AL YLG L
Sbjct: 239 EALVKTEPFTQWVVEDDFCNRRPPLDEVGVQMTNDVASWELVKLRLLNGAHSALAYLGGL 298

Query: 313 KGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLE 372
            G+ +VH+ M  P F   + A  D +    L P+ G D  +Y+  L  RF+N A+  +  
Sbjct: 299 AGHHYVHQAMAAPGFSRLVEALWD-EAEATLKPIDGFDAKNYRAQLAQRFTNSALEHRTH 357

Query: 373 RVCSDGSSKFPKFTVPTINRLIADGRETERA-ALVVAAWALYLKGVDENGVSYTIPDPRA 431
           ++  DGS K P+  + TI       R   +A  + +A W  +  G ++ G ++ + DP A
Sbjct: 358 QIAMDGSQKIPQRWLNTIRAYREADRGVPKALVMALAGWMHWQAGKNDAGETHIVDDPLA 417

Query: 432 EFCQGLVSDDALISQR----LLAVEEIFGTAIPNSPEFVAAFERCYGSL 476
                 + + A    R    LL +  IFG A+P    FV      Y S+
Sbjct: 418 ARTAAALREAAGDRMREVANLLGISAIFGEALPADNAFVQHLTEAYCSI 466


Lambda     K      H
   0.321    0.137    0.414 

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: 596
Number of extensions: 27
Number of successful extensions: 5
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: 493
Length of database: 486
Length adjustment: 34
Effective length of query: 459
Effective length of database: 452
Effective search space:   207468
Effective search space used:   207468
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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