GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Lentibacillus jeotgali Grbi

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_010532097.1 ON01_RS16395 aldehyde dehydrogenase family protein

Query= BRENDA::P05091
         (517 letters)



>NCBI__GCF_000224785.1:WP_010532097.1
          Length = 506

 Score =  367 bits (942), Expect = e-106
 Identities = 209/484 (43%), Positives = 285/484 (58%), Gaps = 22/484 (4%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           +I  E+    + K F  V+P TG+V C++A   KEDV+ AV A  AA      W +   +
Sbjct: 22  YIGGEYRPPANGKYFENVSPVTGKVFCELARSTKEDVEAAVDAGYAA---KDAWAQTSVA 78

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            R  +LN++AD +E +   LA  ET DNGK        D+ + +   RY+AG      G 
Sbjct: 79  ERADILNKIADRMEENLESLAVAETWDNGKAVREGLAADIPLAVDHFRYFAGAIRAQEGG 138

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
              ID D  +Y  HEP+GV GQIIPWNFP+LM  WKL PALA GN VV+K AEQTP +  
Sbjct: 139 VSQIDNDTVAYHFHEPLGVVGQIIPWNFPILMATWKLAPALAAGNCVVLKPAEQTPASIH 198

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279
            + +LIK+   P GV+NIV GFG  AG  +AS+  + K+AFTG T  GR+I   A S N+
Sbjct: 199 VLLDLIKDL-LPAGVLNIVNGFGVEAGKPLASNSRISKIAFTGETTTGRLIMQYA-SENI 256

Query: 280 KRVTLELGGKSPNIIM------SDADMDWAVE-QAHFALFFNQGQCCCAGSRTFVQEDIY 332
             VTLELGGKSPNI         D  +D A+E    FAL  NQG+ C   SR  V E IY
Sbjct: 257 IPVTLELGGKSPNIFFPDVMDKDDGFLDKAIEGLVMFAL--NQGEVCTCPSRALVHESIY 314

Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGI-- 390
           DEF+ER++ R     +G+P D+ T  G Q    Q +KI  Y++ G+QEGA++L GGG+  
Sbjct: 315 DEFMERAIKRVNEIKIGHPLDTDTMMGAQASLEQMEKIKSYLDIGRQEGAEVLVGGGVNQ 374

Query: 391 ---AADRGYFIQPTVF-GDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAA 446
                + GY+I+PT+F GD  + M I +EEIFGPV+ +  F   +E +  AN++ YGL A
Sbjct: 375 LKGDMEEGYYIEPTIFKGD--NKMRIFQEEIFGPVLAVTTFNENDEAMKIANDTLYGLGA 432

Query: 447 AVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVK 506
            V+T++++ A    + ++AG VW+NCY  + A + FGGYK SG GRE     L  Y + K
Sbjct: 433 GVWTRNINTAYRFGRGIEAGRVWMNCYHQYPAHAAFGGYKKSGIGRENHLMMLDHYQQTK 492

Query: 507 TVTV 510
            + +
Sbjct: 493 NLLI 496


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: 633
Number of extensions: 33
Number of successful extensions: 7
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: 506
Length adjustment: 35
Effective length of query: 482
Effective length of database: 471
Effective search space:   227022
Effective search space used:   227022
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 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