GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Ruegeria conchae TW15

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_010438474.1 G7G_RS0103600 betaine-aldehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>NCBI__GCF_000192475.1:WP_010438474.1
          Length = 484

 Score =  343 bits (879), Expect = 1e-98
 Identities = 177/474 (37%), Positives = 271/474 (57%), Gaps = 5/474 (1%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           HFI+G++V    G   D I PAT E +  +       ++ A+ +AK A    W  M+  E
Sbjct: 9   HFINGEYVEDTRGTPIDVIYPATGEVIARLHSATPEIVEQALNSAKSA-QASWAAMSGTE 67

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R  VLR+  D++ +R   LS+LE+ DTGKP   +   D    A    +F     ++T E 
Sbjct: 68  RGRVLRRASDIMRDRNRALSILETHDTGKPLQETLVADATSGADALEYFGSLAASLTGEH 127

Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192
             +      Y IR  +GV   I  WN P  +  WK APALA GN +V KP+E TP++A  
Sbjct: 128 IPLGGGDFVYTIREALGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLSALQ 187

Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252
           +AEI  +AG P G+ N+V G+G    GA+L   P V  +S TG   TG+ + A+AA  +K
Sbjct: 188 VAEILIEAGAPKGIYNVVQGYG--DVGASLVTDPRVAKVSLTGSVPTGRKVYAAAADGMK 245

Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312
            ++ ELGGK+P ++F D++LD  +   +  +F + G+VC  G+R++V++   EAFL +  
Sbjct: 246 HVTMELGGKSPMIVFDDADLDNAVSGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLSRLS 305

Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFL 372
            +     +GDP D +   G ++S+       GY++    EG  ++ GG R  G   G+++
Sbjct: 306 DRLATAKIGDPLDEEVNFGPMVSENQMNIALGYVEKGKAEGARLVYGGVRIAG--DGFYM 363

Query: 373 EPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHR 432
           +PT+   +T D  + +EEIFGPV++V+ F+TEEEVL + NDT +GL+A V+TNDL RAHR
Sbjct: 364 QPTVFADVTDDMTIAREEIFGPVMSVLDFETEEEVLARANDTEFGLAAGVFTNDLTRAHR 423

Query: 433 VAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486
           +    EAG  ++NT+ L  +  PFGG K SG+GRE    +   +SE+  + + +
Sbjct: 424 IVAGFEAGTCYINTYNLAPVEAPFGGSKMSGVGRENSKLAINHFSEMKTVYVSM 477


Lambda     K      H
   0.318    0.136    0.404 

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: 592
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: 486
Length of database: 484
Length adjustment: 34
Effective length of query: 452
Effective length of database: 450
Effective search space:   203400
Effective search space used:   203400
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