GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Burkholderia phytofirmans PsJN

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BPHYT_RS29875 BPHYT_RS29875 betaine-aldehyde dehydrogenase

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__BFirm:BPHYT_RS29875
          Length = 483

 Score =  422 bits (1084), Expect = e-122
 Identities = 217/459 (47%), Positives = 294/459 (64%), Gaps = 6/459 (1%)

Query: 57  VNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDR 116
           +NP+T E I  VA+G   DVD AV+AARAA ++   W  +  + R R+L RLA L+  + 
Sbjct: 30  INPATEEPIALVAQGSAADVDTAVRAARAALKV---WNGIRTAERARILMRLAGLMRANL 86

Query: 117 TYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPV 176
             LAALE+LD GKP       D+   +  L YYAGW DK +G+ +P+  D  +YT  EPV
Sbjct: 87  EELAALESLDAGKPIAAVMRQDIPAAIDTLEYYAGWCDKINGQVVPVRPDALTYTLREPV 146

Query: 177 GVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGVVN 236
           GV   I+PWNFPL++  WK+ PALA G  +++K AE TPLTAL +  L  EAG PPGV+N
Sbjct: 147 GVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLTALRIGELALEAGVPPGVLN 206

Query: 237 IVPGFGPTAGAAIASHEDVDKVAFTGSTEIGR-VIQVAAGSSNLKRVTLELGGKSPNIIM 295
           IV G G   G A+ +H  VDKV FTGS  +GR ++Q AAG  N KRVTLELGGKS N+I 
Sbjct: 207 IVTGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAAG--NFKRVTLELGGKSANLIF 264

Query: 296 SDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGNPFDSK 355
            DA++D AV  A   +FFN GQ C AGSR     D+YDE VER  ARAKS  VG+P   +
Sbjct: 265 PDANLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVERLAARAKSIKVGDPSSRE 324

Query: 356 TEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVFGDVQDGMTIAKE 415
           T  GP +   Q K +LGY+ TG+ EGA L+ GG    +RG+F++PTVF +V+  M I++E
Sbjct: 325 TSMGPLISAAQMKTVLGYVETGRAEGASLVTGGARVGERGFFVEPTVFANVEHEMRISQE 384

Query: 416 EIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDV 475
           EIFGPV  +++F    + +  AN + Y LAA V++ D+ + + +++ L+AGTVW+N Y  
Sbjct: 385 EIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRVHRVARDLRAGTVWINTYGY 444

Query: 476 FGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKVPQ 514
              + P+GG   SG GRE G+  ++ +TE K V + + Q
Sbjct: 445 TDVRLPWGGSGDSGFGREHGDVAIENFTEPKAVWLAIDQ 483


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: 651
Number of extensions: 25
Number of successful extensions: 3
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: 483
Length adjustment: 34
Effective length of query: 483
Effective length of database: 449
Effective search space:   216867
Effective search space used:   216867
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