GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Nocardioides daejeonensis MJ31

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_110207793.1 DNK54_RS15005 aldehyde dehydrogenase

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



>NCBI__GCF_003194585.1:WP_110207793.1
          Length = 501

 Score =  355 bits (911), Expect = e-102
 Identities = 196/478 (41%), Positives = 287/478 (60%), Gaps = 9/478 (1%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKA-LNGPWKKMTAN 71
           +FI+G +  +  G+  +  +PAT E + TVA+GGAAEID AV AAK A   G W+     
Sbjct: 8   NFINGAWTDN--GQVLEVRSPATGELVATVAKGGAAEIDAAVAAAKAAHAAGVWRNTPPA 65

Query: 72  ERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNE 131
           ER A++  V   +  R EEL+ L+S + G    ++G++ +  +  N  F +        E
Sbjct: 66  ERAALINAVAGDLAGRLEELAALQSRENGATIRVTGALHVGLSIANMQFIAAQAAEYEFE 125

Query: 132 AT--QMDDVALNYAIRR-PVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPM 188
               ++  V     +RR P+GV+G I PWN+PLL + WK+ PALAAGNTVV+KP E  P+
Sbjct: 126 KAGPEIGPVPAEGILRREPLGVVGAIVPWNIPLLTIVWKVTPALAAGNTVVLKPDEHAPL 185

Query: 189 TATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAA 248
            A  LA+    AG+P GV+N+V G G + AGA L++HPDV  I FTG T  GK I+ ++A
Sbjct: 186 LALELAKAFEAAGLPAGVLNVVVGEG-HDAGARLSQHPDVRKIGFTGSTEVGKSILGASA 244

Query: 249 KTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFL 308
             +KR++ ELGGK PN++  D++LD  I+  + +   N GE C  G+R+ V     +  +
Sbjct: 245 DNMKRVTLELGGKGPNILLDDADLDVAIDGAIYACMANNGEACEAGTRLLVPNSRKDEIV 304

Query: 309 EKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLE- 367
           E+ VA+   + +G+P D  T +G LI+ +  +RV  +I  A  +G  +  GG  P G E 
Sbjct: 305 ERLVARVGTMKIGNPLDPATDIGPLITADQRDRVLAHIAKAETQGAKVAIGGSAPAGEEF 364

Query: 368 -KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTND 426
             GYF+EPT++T +T    V  EE+FGPV++V+ +DT +E +   NDT YGLSA VW  D
Sbjct: 365 ANGYFVEPTVLTDVTPSMTVACEEVFGPVLSVLGYDTVDEAIAIANDTEYGLSAGVWGTD 424

Query: 427 LRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484
             R   VA Q+EAG+++VN W +     PFGG KQSG+GREGG ++ + Y+E   I +
Sbjct: 425 ETRVLDVARQLEAGMIYVNDWHVLHPAYPFGGYKQSGLGREGGPNALDAYTEQKYISV 482


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: 692
Number of extensions: 29
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: 501
Length adjustment: 34
Effective length of query: 452
Effective length of database: 467
Effective search space:   211084
Effective search space used:   211084
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