GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Lentibacillus jeotgali Grbi

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_010532097.1 ON01_RS16395 aldehyde dehydrogenase family protein

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_000224785.1:WP_010532097.1
          Length = 506

 Score =  302 bits (774), Expect = 2e-86
 Identities = 171/462 (37%), Positives = 259/462 (56%), Gaps = 13/462 (2%)

Query: 23  NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82
           +P TG V  E+A ++ E V+AAV A  AA   W QT+   RA+ L K+AD +EEN +  A
Sbjct: 40  SPVTGKVFCELARSTKEDVEAAVDAGYAAKDAWAQTSVAERADILNKIADRMEENLESLA 99

Query: 83  ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIRRDPLGVV 142
             E+ + GK +      +IP  VD FR+FAGA R   G    +      +    +PLGVV
Sbjct: 100 VAETWDNGKAVREGLAADIPLAVDHFRYFAGAIRAQEG-GVSQIDNDTVAYHFHEPLGVV 158

Query: 143 ASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVINILFG 202
             I PWN+P++MA WKLAPALAAGNCVVLKP+E TP +   L +L KD+ PAGV+NI+ G
Sbjct: 159 GQIIPWNFPILMATWKLAPALAAGNCVVLKPAEQTPASIHVLLDLIKDLLPAGVLNIVNG 218

Query: 203 RGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVF------ 256
            G   G PL  + ++  ++ TG   TG  I+ + + +I    +ELGGK+P I F      
Sbjct: 219 FGVEAGKPLASNSRISKIAFTGETTTGRLIMQYASENIIPVTLELGGKSPNIFFPDVMDK 278

Query: 257 DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDES 316
           DD  ++  +EG+  F   N G+ CT   R    + IYD  +E+    V  +K G P D  
Sbjct: 279 DDGFLDKAIEGLVMFA-LNQGEVCTCPSRALVHESIYDEFMERAIKRVNEIKIGHPLDTD 337

Query: 317 TELGPLSSLAHLERVGKAVEEAKATGHIKVITGG-EKRKGN---GYYYAPTLLAGALQDD 372
           T +G  +SL  +E++   ++  +  G   ++ GG  + KG+   GYY  PT+  G     
Sbjct: 338 TMMGAQASLEQMEKIKSYLDIGRQEGAEVLVGGGVNQLKGDMEEGYYIEPTIFKGD-NKM 396

Query: 373 AIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWV 432
            I Q+E+FGPV++VT F+  ++ +  AND+ YGL + VWT+++  A+R    ++ G  W+
Sbjct: 397 RIFQEEIFGPVLAVTTFNENDEAMKIANDTLYGLGAGVWTRNINTAYRFGRGIEAGRVWM 456

Query: 433 NTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
           N +    +    GG K SG G++  L  L+ Y   +++++ +
Sbjct: 457 NCYHQYPAHAAFGGYKKSGIGRENHLMMLDHYQQTKNLLISY 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: 600
Number of extensions: 26
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 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