GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Dinoroseobacter shibae DFL-12

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__Dino:3607686
          Length = 506

 Score =  359 bits (921), Expect = e-103
 Identities = 208/483 (43%), Positives = 283/483 (58%), Gaps = 20/483 (4%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           FI  ++   V  + F  V P TGEV+ Q+A     DV+ A+ AA AA      W +   +
Sbjct: 22  FIGGKFVPPVEGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAA---KDAWGKTSVT 78

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            R  ++ ++AD IE +   +A  ET DNGKP   + L D+ + +   RY+AG      G 
Sbjct: 79  ERANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRGQEGS 138

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
              ID D  +Y  HEP+GV GQIIPWNF +LM AWKL PA+A GN +V+K AEQTP   +
Sbjct: 139 MSEIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQTPAAIM 198

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279
            +  LI +   P GV+NIV G+G   GAA+A+ + + K+AFTGST  GR I  AA + NL
Sbjct: 199 VLVELISDL-LPAGVLNIVNGYGGEVGAALATSDRIAKIAFTGSTATGRKIMEAA-TVNL 256

Query: 280 KRVTLELGGKSPNIIM------SDADMDWAVEQAHFALF-FNQGQCCCAGSRTFVQEDIY 332
             VTLELGGKSPNI         DA +D AVE   F LF FNQG+ C   SR  + EDIY
Sbjct: 257 IPVTLELGGKSPNIFFKDVMAEDDAFLDKAVE--GFVLFAFNQGEVCTCPSRALIHEDIY 314

Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIA- 391
           +EF+ R++AR K+ V G+P   +T  G Q  + Q  KIL Y   G +EGA++L GG +A 
Sbjct: 315 EEFIARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTGGKVAD 374

Query: 392 ----ADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAA 447
                  G++I+PT+     + M + +EEIFGPV+ +  FKT EE +  AN++ YGL A 
Sbjct: 375 VSDDLKDGFYIEPTILKG-HNKMRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGLGAG 433

Query: 448 VFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKT 507
           V+++D +      + +QAG VWVN Y  + A + FGGYK SG GRE  +  L  Y + K 
Sbjct: 434 VWSRDQNTCYRFGRGVQAGRVWVNNYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKN 493

Query: 508 VTV 510
           + V
Sbjct: 494 MLV 496


Lambda     K      H
   0.319    0.136    0.409 

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: 608
Number of extensions: 20
Number of successful extensions: 6
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: 517
Length of database: 506
Length adjustment: 35
Effective length of query: 482
Effective length of database: 471
Effective search space:   227022
Effective search space used:   227022
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 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