GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Methylocystis bryophila S285

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_002117405.1:WP_085772038.1
          Length = 506

 Score =  308 bits (790), Expect = 2e-88
 Identities = 177/470 (37%), Positives = 261/470 (55%), Gaps = 15/470 (3%)

Query: 16  GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIE 75
           GE     +P TG  + ++A   A  V+ A+ AA  A   WG+T    RA  L K+A  ++
Sbjct: 33  GEYFDNISPITGHPICQVARGRAADVELALDAAHKAKDAWGKTPAAERANMLNKIAQRLD 92

Query: 76  ENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIR 135
           +N    A +E+ + GKP+      +IP  +D FR+FAG  R   G +  E      +   
Sbjct: 93  DNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQEG-SLSEIDHDTVAYHF 151

Query: 136 RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAG 195
            +PLGVV  I PWN+P++MAAWKL+PALAAGNCVVLKP+E TP++ L +AEL  D+ P G
Sbjct: 152 HEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTPMSILAVAELIADLLPPG 211

Query: 196 VINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIV 255
           V+NI+ G G   G PL  + ++  ++ TG   TG  I+ + A ++    +ELGGK+P I 
Sbjct: 212 VLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYAAENLIPVTLELGGKSPNIF 271

Query: 256 F------DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKS 309
           F      DDA ++  +EG  +F   N G+ CT   R   Q+ IYD  +EK  A VA ++ 
Sbjct: 272 FADVMAEDDAFLDKALEGFASFA-LNQGEVCTCPSRALVQRSIYDKFMEKALARVAKIRQ 330

Query: 310 GAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEK-----RKGNGYYYAPTL 364
           G P D +T +G  +S   LE++   V+  +  G  KV+ GGE+         GYY  PT 
Sbjct: 331 GHPLDPATMIGAQASNDQLEKILSYVDIGRKEG-AKVLIGGERSVLEGELKEGYYMQPTA 389

Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424
           L G      + Q+E+FGPVVSVT F+ EE+ +  AND+ YGL + +WT+D  RA+R    
Sbjct: 390 LEGH-NRMRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGAGLWTRDGSRAYRCGRA 448

Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
           ++ G  W N +    +    GG K SG G++     L+ Y   ++++V +
Sbjct: 449 IRAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNLLVSY 498


Lambda     K      H
   0.317    0.134    0.397 

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: 595
Number of extensions: 29
Number of successful extensions: 4
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: 474
Length of database: 506
Length adjustment: 34
Effective length of query: 440
Effective length of database: 472
Effective search space:   207680
Effective search space used:   207680
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 Apr 09 2024. 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