GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Erythrobacter gangjinensis K7-2

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_047007132.1 AAW01_RS09770 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_001010925.1:WP_047007132.1
          Length = 476

 Score =  325 bits (832), Expect = 3e-93
 Identities = 180/464 (38%), Positives = 268/464 (57%), Gaps = 9/464 (1%)

Query: 46  LLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISV 105
           L+ G+   GG       T  V +PA+   LGT+      +   A+ AA   F  W+  S 
Sbjct: 10  LIAGEKVTGGG----RDTEEVINPATEEVLGTLPHATSDDLDRALDAAQSGFREWRSTSA 65

Query: 106 KERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGD 165
            +R+++L    +L+ + K+++A  +T E GKPL + +GE +YSA  LE++++EA+R YG 
Sbjct: 66  DKRATILTNAANLIRERKEDIAGWLTREQGKPLGDGRGEAMYSANLLEFYAQEAKRTYGR 125

Query: 166 IIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSA 225
            +    +  R  V   PVG  +   PWNFP+  + RK+G ALAAGC+V+VKP+E+TP + 
Sbjct: 126 TL-VRGEGSRVEVQYHPVGPVAGFAPWNFPAINVMRKIGGALAAGCSVIVKPSEETPAAG 184

Query: 226 LALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAA 285
           +AL Q    AG+P G    + C       V E L   P++ K++FTGST  GK L   AA
Sbjct: 185 IALVQALLDAGVPGGA---VQCVFGVPSNVSEHLLASPIIRKLTFTGSTPVGKHLAKLAA 241

Query: 286 NSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFV 345
           + +K  +MELGG  P +VFD  +VD+AV     +K+RNAGQ CV   RFL++  I + F 
Sbjct: 242 DDLKITTMELGGHGPVLVFDDCDVDKAVKTMAGNKYRNAGQVCVSPIRFLIEESIFEQFR 301

Query: 346 TKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGG 405
             F E  +K +RVGNG E+GT  GP+ N +  E ++K + +A   GA ++TGG+   + G
Sbjct: 302 DSFVERAEK-VRVGNGLEDGTDMGPMANARGRENIQKLIANAKEAGANLLTGGEVIGNQG 360

Query: 406 NFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQ 465
            F +PT+LS V      +  E FGPVA +     E+  +  AN    GLA Y ++ D A+
Sbjct: 361 FFHQPTVLSEVPTSADIMNNEPFGPVAILNPMSGEDAMIEEANRLPYGLAAYAWTDDAAR 420

Query: 466 IWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGI 509
             R+A ++E GM+ +N G +S+V+ PFGGVK SG G E  + G+
Sbjct: 421 RRRLAAEVEAGMLAINGGSVSTVDAPFGGVKWSGYGSEDGREGV 464


Lambda     K      H
   0.318    0.135    0.400 

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: 607
Number of extensions: 23
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: 523
Length of database: 476
Length adjustment: 34
Effective length of query: 489
Effective length of database: 442
Effective search space:   216138
Effective search space used:   216138
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