Alignments for a candidate for pad-dh in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pad-dh in Paraburkholderia bryophila 376MFSha3.1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate H281DRAFT_01117 H281DRAFT_01117 aldehyde dehydrogenase (NAD+)

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__Burk376:H281DRAFT_01117
          Length = 795

 Score =  370 bits (951), Expect = e-107
 Identities = 212/469 (45%), Positives = 283/469 (60%), Gaps = 26/469 (5%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           FI   WH   S   F +  P++GE +  +A+GD  D+D A+ AARAA Q G  W  +   
Sbjct: 36  FIGGAWHAPASGAQFVSHAPASGERLADIAQGDAADIDAALAAARAA-QPG--WLALGGK 92

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            R R L  LA +++R     A LE LDNGKP   +  +D+ +V +   ++AGWA     +
Sbjct: 93  GRARHLYALARMVQRHSRLFAVLEALDNGKPIRETRDLDVPLVARHFLHHAGWAQLQDSE 152

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
                     +  H P+GV GQI+PWNFPLLM AWK+ PA+ATGN VV+K AE TPLTAL
Sbjct: 153 ----------FADHAPLGVIGQIVPWNFPLLMLAWKIAPAIATGNCVVLKPAEYTPLTAL 202

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQ-VAAGSSN 278
             A L  +AG P GV+N+V G G T GAA+  H  VDK+AFTGSTE+G++I+ V AGS  
Sbjct: 203 LFAELAHQAGLPAGVLNVVTGDGST-GAALVEHPQVDKIAFTGSTEVGKLIRSVTAGSG- 260

Query: 279 LKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338
            K +TLELGGKSP I+  DAD+D AVE    A++FNQGQ CCAGSR  VQE I   F+ +
Sbjct: 261 -KSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVCCAGSRLLVQEGIEARFIAK 319

Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD----- 393
              R ++  VG   D   + G  VD  Q ++I   + TG++EG    C    AAD     
Sbjct: 320 LKRRMETLRVGPSLDKSIDMGAIVDPVQLERIHSLVETGRREG----CAIWQAADTPLPA 375

Query: 394 RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDL 453
            G F  PT+  +V    T+A+EEIFGPV+  + F+T +E +  ANNS YGLAA+V+++ +
Sbjct: 376 NGCFYPPTLVTNVAPASTLAQEEIFGPVLVTMSFRTPDEAIALANNSRYGLAASVWSETI 435

Query: 454 DKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAY 502
            +A  ++  L AG VWVN  ++F A   FGGY+ SG GRE G  G+  Y
Sbjct: 436 GRALDVAPRLAAGVVWVNATNLFDAAVGFGGYRESGYGREGGREGIHEY 484



 Score = 98.6 bits (244), Expect = 8e-25
 Identities = 77/233 (33%), Positives = 112/233 (48%), Gaps = 10/233 (4%)

Query: 57  VNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDR 116
           V+   G  + +V EG+++D+  AV+AARAA      W +    +R ++L  LA+ +    
Sbjct: 540 VHAPDGTRVGEVGEGNRKDIRNAVQAARAA----QKWSQASTHNRAQVLFYLAENLAVRA 595

Query: 117 TYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK--TIPIDGDFFSYTRHE 174
              A   T+ NG     ++  +++  +  L  YA WADK+ G   T P+ G   +   HE
Sbjct: 596 DEFAHQLTVRNGATDAAAH-AEVEASVTRLFTYAAWADKFDGAVHTPPLRG--VALAMHE 652

Query: 175 PVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGV 234
           P+GV G   P   PLL       PALA GN VV+   E  PL       +++ +  P GV
Sbjct: 653 PLGVIGIACPDEAPLLAFVSLAAPALAMGNRVVVLPGEACPLAVTDFYQVVETSDVPGGV 712

Query: 235 VNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELG 287
           VNIV G       A+A H+DVD V   GS     +I+      NLKR   + G
Sbjct: 713 VNIVTGKREALLPALARHDDVDAVWCFGSAADATLIE-RESVGNLKRTFTDYG 764


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: 966
Number of extensions: 57
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 517
Length of database: 795
Length adjustment: 38
Effective length of query: 479
Effective length of database: 757
Effective search space:   362603
Effective search space used:   362603
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources