GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Nocardioides daejeonensis MJ31

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_110207251.1 DNK54_RS12190 aldehyde dehydrogenase family protein

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_003194585.1:WP_110207251.1
          Length = 474

 Score =  239 bits (609), Expect = 2e-67
 Identities = 147/468 (31%), Positives = 234/468 (50%), Gaps = 6/468 (1%)

Query: 6   KLKNYINGEWVESKTDQYEDVVNPATK-EVLCQVPISTKEDIDYAAQTAAEAFKTWSKVA 64
           K++ ++ GEW  + T    +  NPA   EV+     +T +D+  A   A +A + W +  
Sbjct: 4   KIRQFVGGEW-RAGTGSAIESRNPARPHEVVASGHAATPDDVTEAVAAATKAAQAWRRTL 62

Query: 65  VPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMG 124
           +  RA +L    +LL +  + L   +T+E GK   E +GEV R  E   F AG     +G
Sbjct: 63  MHERAAVLRRTAELLEERADALGLELTLEEGKTLVEGIGEVRRAAEIFRFNAGQADREVG 122

Query: 125 DSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLL 184
           +  AS          R PIGVV  I P+NFP+ +P W    A+  GN  + KP+   PLL
Sbjct: 123 EVFASPRRGERIVVTRKPIGVVAVITPWNFPIAIPAWKIAPALIHGNAVVWKPASIVPLL 182

Query: 185 TEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENL 244
             +L E    AGLP GV +++ G   + + I   P + A++F GS  +G  + +  +   
Sbjct: 183 AVRLAEALHDAGLPAGVLSLIIGPGALGSQIASAPGVHAVTFTGSTGIGTGLLQLCAPLR 242

Query: 245 KRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304
           + VQ+  G KN  +V  DA+LE     IV  A  S G++C A + + VE+ +A++    L
Sbjct: 243 RPVQAEMGGKNAAVVFADADLELAADQIVLGAMRSTGQKCTATSRLVVEDSVAEDLRTLL 302

Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFV 364
            +++  + +G+G    V +GPV     +    S I+  L  GAR+V   +    DDG++V
Sbjct: 303 VQRIEALVVGDGTRSDVTVGPVSSGGAQAEITSMIDDALRGGARVV--AQAEAPDDGHYV 360

Query: 365 GPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRY 424
            PTI + V     IW++E+F PVL++    +    +E+AN SEF   A +FTS+ +    
Sbjct: 361 PPTILE-VDVRQPIWREEVFGPVLAMTTGADEDRVLELANASEFGLSAAVFTSDLSRTLR 419

Query: 425 FRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYT 472
             + ++ G+L +N          PF G K S  G     G+ S +F+T
Sbjct: 420 IMDELEVGVLHVNSESAGADPHVPFGGVKDSGIGP-KEQGRASREFFT 466


Lambda     K      H
   0.318    0.136    0.396 

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: 502
Number of extensions: 20
Number of successful extensions: 3
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: 487
Length of database: 474
Length adjustment: 34
Effective length of query: 453
Effective length of database: 440
Effective search space:   199320
Effective search space used:   199320
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. 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