GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Dechlorosoma suillum PS

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Dsui_1464 Dsui_1464 NAD-dependent aldehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>FitnessBrowser__PS:Dsui_1464
          Length = 506

 Score =  347 bits (889), Expect = e-100
 Identities = 193/481 (40%), Positives = 280/481 (58%), Gaps = 14/481 (2%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           +FI GK+V  + G+ FD I P T +     A+ GA +I+LA+ AA  A +  W K +A E
Sbjct: 21  NFIGGKWVAPVKGQYFDVITPITGKPYTQAAQSGAEDIELALDAAHAAAD-KWGKTSATE 79

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R  +L K+ D I    E L+ +E++D GK    + + DIP AA +F +F+  +R+     
Sbjct: 80  RSNILLKIADRIEANLEMLAYVETVDNGKAIRETLNADIPLAADHFRYFAGCLRSQEGSI 139

Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192
           +++D+  + Y    P+GV+G I PWN P+L+  WKLAPAL AGN VV+KPAE TP++  V
Sbjct: 140 SEIDENTIAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALGAGNCVVLKPAESTPISILV 199

Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252
           LAE+  D  +P GV+N+V+G+G   AG AL     +  I+FTG T TG++I  +AA +L 
Sbjct: 200 LAELIADL-LPPGVLNIVNGYG-RDAGMALASSKRIAKIAFTGSTATGRVIAQAAANSLI 257

Query: 253 RLSYELGGKNPNVIFA------DSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEA 306
             + ELGGK+PN+ FA      D   D+ IE  +  +F NQGEVC C SR  +    Y+ 
Sbjct: 258 PATLELGGKSPNIFFADVAAADDDFFDKAIEGLVLFAF-NQGEVCTCPSRALIHESIYDH 316

Query: 307 FLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE-- 364
           F+E+ +A+ K +  G P D  + +GA  S    +++  Y+ +  EEG   L GG R    
Sbjct: 317 FMERVLARVKAIKQGSPLDTDSMMGAQASQMQMDKIMSYLAIGKEEGAQCLVGGDRARLG 376

Query: 365 -GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423
             L +GY+++PT+  G  +  R+ +EEIFGPV+ V  F TE E LE  NDT YGL A VW
Sbjct: 377 GELAEGYYIQPTLFKGHNK-MRIFQEEIFGPVLAVTTFKTEAEALEIANDTPYGLGAGVW 435

Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNIC 483
           + D   A+R+   I+AG VW N +        FGG K+SGIGRE      + Y +  N+ 
Sbjct: 436 SRDGNTAYRMGRGIKAGRVWTNCYHAYPAHATFGGYKESGIGRETHKMMLDHYQQTKNLL 495

Query: 484 I 484
           +
Sbjct: 496 V 496


Lambda     K      H
   0.318    0.136    0.404 

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: 568
Number of extensions: 27
Number of successful extensions: 7
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: 486
Length of database: 506
Length adjustment: 34
Effective length of query: 452
Effective length of database: 472
Effective search space:   213344
Effective search space used:   213344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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