GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Pseudomonas simiae WCS417

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF5420 PS417_27745 aldehyde dehydrogenase

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



>FitnessBrowser__WCS417:GFF5420
          Length = 497

 Score =  360 bits (924), Expect = e-104
 Identities = 197/488 (40%), Positives = 288/488 (59%), Gaps = 4/488 (0%)

Query: 2   QQTKVKPIDCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKAL 61
           Q+ K   I+   +I+G++  ++ G TF+ I+P     L TVA   AA+   AV+ A+   
Sbjct: 11  QRAKDLKIEGRAYINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQRAVENARATF 70

Query: 62  N-GPWKKMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHF 120
           N G W ++   +R + + +   L+    EEL++LE+LD GKP   S +ID+P AA    +
Sbjct: 71  NSGVWSRLAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPGAANALSW 130

Query: 121 FSDYIRTITNEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVM 180
             + I  I +E        L    R PVGV+G I PWN PL++  WKL PAL+ GN+V++
Sbjct: 131 SGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVIL 190

Query: 181 KPAELTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTG 240
           KP+E +P+TA  +A +  +AG+P GV N++ G+G ++ G AL  H DV+ + FTG T   
Sbjct: 191 KPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYG-HTVGNALALHMDVDTLVFTGSTKIA 249

Query: 241 K-IIMASAAKTLKRLSYELGGKNPNVIFADS-NLDEVIETTMKSSFINQGEVCLCGSRIY 298
           K +++ S    +KR+  E GGK+PN++FAD+ +L    E+   +   NQGEVC  GSR+ 
Sbjct: 250 KQLLIRSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTAGSRLL 309

Query: 299 VERPAYEAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILT 358
           VER   + FL   +   K    G+P D  T VGAL+  +    V  YI+    +G  ++ 
Sbjct: 310 VERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHADGAKLVA 369

Query: 359 GGKRPEGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGL 418
           GGKR      G ++EPTI  G+T   ++ KEEIFGPV++VI FD+ EE +   NDT YGL
Sbjct: 370 GGKRTLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIANDTIYGL 429

Query: 419 SASVWTNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478
           +A+VWT D+ +AH  A  + AG VWVN +   D+  PFGG KQSG GR+  LH+F+ Y+E
Sbjct: 430 AAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTE 489

Query: 479 LTNICIKL 486
           L    IKL
Sbjct: 490 LKATWIKL 497


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: 625
Number of extensions: 23
Number of successful extensions: 5
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: 497
Length adjustment: 34
Effective length of query: 452
Effective length of database: 463
Effective search space:   209276
Effective search space used:   209276
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 17 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