GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Salinicoccus carnicancri Crm

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_017549894.1 C792_RS0113000 aldehyde dehydrogenase family protein

Query= BRENDA::Q8VWZ1
         (503 letters)



>NCBI__GCF_000330705.1:WP_017549894.1
          Length = 476

 Score =  342 bits (876), Expect = 2e-98
 Identities = 194/487 (39%), Positives = 293/487 (60%), Gaps = 20/487 (4%)

Query: 6   SSRQLFIDGEWRVPILNKRIPNINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRD 65
           +S Q FIDGEW      + I  INP+TE+++G I   T+EDV+ AV+AAK+A       D
Sbjct: 3   TSNQQFIDGEWVNSTSQETIEVINPATESVMGTIAKGTQEDVNKAVEAAKKAYI-----D 57

Query: 66  WSAASGSLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEALADLDDVVACFEYYAGLA 125
           +       R   L  I  + K++K ++ +  + + G P E  L++    +    +++   
Sbjct: 58  FRQTPTKERQDMLNRIVEEYKKRKTDIIEAITEELGSPRE--LSETTHYMKGLIHFSEAR 115

Query: 126 EELDS---KQKAPISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAA 182
           + LD    K+K   SL        I+KE IGV  L+TPWN+P    + K+A A AAG   
Sbjct: 116 DALDDFAFKEKRGDSL--------IVKEGIGVTGLVTPWNFPTNQTSVKLAAAFAAGSPV 167

Query: 183 ILKPSELASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSAT 242
           ILKPS       + L E+ +  G+P+GV N+V G G   G +L+SHPDV  +SFTGS + 
Sbjct: 168 ILKPSVETPFAAIILAEVIQASGVPKGVFNLVNGRGSVIGDALSSHPDVRMMSFTGSESA 227

Query: 243 GSKIMTTAAQLVKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIV 302
           GSKIM  ++Q  K VSLELGGKSP ++ +DVD+DK A+      +  +GQ+C A +R ++
Sbjct: 228 GSKIMRNSSQDFKRVSLELGGKSPYIILDDVDVDKAAKSATKFVYDNSGQVCDAATRTLI 287

Query: 303 HESIAVEFVDKLVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTG 362
            ESI  EF++K  +  E++++ +P E+   +GP+VS  Q+  V   I     EGAT++TG
Sbjct: 288 PESIKDEFIEKAKQNMESVRVGNPNEKNMDIGPLVSRQQFNAVQGYIKKGIDEGATLITG 347

Query: 363 G-RRPEHLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGL 421
           G  +PE L++GY+V+PTI +DV   M I +EE+FGPV+++ T+ST +EAI++ANDT++GL
Sbjct: 348 GLGKPEGLERGYYVKPTIFSDVDNDMTIAKEEIFGPVMSIITYSTLDEAIDIANDTNFGL 407

Query: 422 GSAVMSNDLERCERLSKALQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLS 481
              VM  + E  ++++ AL+AG + IN         P+GG K SG GRE G++G+E +L 
Sbjct: 408 CGYVMGENRENVQKVANALEAGSIVIN-ENAGTPDLPFGGYKHSGIGREWGDYGIEEFLE 466

Query: 482 VKQVTRY 488
           VK +  Y
Sbjct: 467 VKALKGY 473


Lambda     K      H
   0.317    0.134    0.402 

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: 509
Number of extensions: 18
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: 503
Length of database: 476
Length adjustment: 34
Effective length of query: 469
Effective length of database: 442
Effective search space:   207298
Effective search space used:   207298
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 (21.6 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