GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Nocardioides daejeonensis MJ31

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_110207396.1 DNK54_RS13100 aldehyde dehydrogenase family protein

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_003194585.1:WP_110207396.1
          Length = 507

 Score =  315 bits (806), Expect = 3e-90
 Identities = 183/463 (39%), Positives = 257/463 (55%), Gaps = 15/463 (3%)

Query: 23  NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82
           +P  G    EIA  +AE ++AAV AA AA   WG+T+   R+  LLK+AD +E +    A
Sbjct: 41  SPVNGKPFTEIARGTAEDIEAAVDAAWAAADAWGRTSTTDRSNILLKIADRMERHLDDLA 100

Query: 83  ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIRRDPLGVV 142
            +E+ + GK +    N ++P  +D FR+FAGA R   G    E  E   +    +PLGVV
Sbjct: 101 VIETWDNGKAVRETLNADLPLAIDHFRYFAGALRGQEG-GISEIDENTVAYHFHEPLGVV 159

Query: 143 ASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVINILFG 202
             I PWN+P++MA WKLAPALAAGNCVVLKP+E TP + LKL EL  D+ PAGV+N++ G
Sbjct: 160 GQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQTPWSILKLVELVGDLLPAGVLNVVNG 219

Query: 203 RGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVFD----- 257
            G   G PL   P++R ++ TG   TG  I+ + + +I    +ELGGK+P I FD     
Sbjct: 220 FGVEAGKPLASSPRIRKIAFTGETTTGRLIMQYASENIIPVTLELGGKSPNIFFDDVATS 279

Query: 258 -DADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDES 316
            DA  +  +EG   F   N G+ CT   R   Q+ +Y   V    A V  +K G P D S
Sbjct: 280 RDAFYDKALEGFTMFA-LNQGEVCTCPSRALVQQSMYADFVPDAIARVEAIKQGNPLDVS 338

Query: 317 TELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKR-----KGNGYYYAPTLLAGALQD 371
           T +G  +S   LE++   +E  K  G  KV+TGGE+         GYY  PT+  G    
Sbjct: 339 TMMGAQASNDQLEKILSYLEIGKQEG-AKVLTGGERNVLEGDLAEGYYVQPTVFEGN-NA 396

Query: 372 DAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTW 431
             I Q+E+FGPVVS+T F +E   +  AND+ YGL + +WT+D  RA R+   +Q G  W
Sbjct: 397 MRIFQEEIFGPVVSLTSFSDEADALQTANDTLYGLGAGLWTRDGSRAFRMGKGIQAGRVW 456

Query: 432 VNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
            N +    +    GG K SG G++     L+ Y   ++++V +
Sbjct: 457 TNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNLLVSY 499


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: 612
Number of extensions: 32
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: 507
Length adjustment: 34
Effective length of query: 440
Effective length of database: 473
Effective search space:   208120
Effective search space used:   208120
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 24 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