GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Luteipulveratus mongoliensis MN07-A0370

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_052591776.1 VV02_RS12055 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_001190945.1:WP_052591776.1
          Length = 486

 Score =  413 bits (1062), Expect = e-120
 Identities = 223/469 (47%), Positives = 302/469 (64%), Gaps = 5/469 (1%)

Query: 52  FVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERS 109
           F+ G W      AT  V +PA+G  L  VAD  V +  AA+ AA  A + W +   ++R 
Sbjct: 17  FIAGEWRDAEGGATLEVDNPATGEALTHVADGSVKDGDAALAAAAAAQADWAKTPPRDRG 76

Query: 110 SLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYT 169
            LLR  Y+++++  ++LA ++T E GKPL E++GE+ Y + F  WFSEEA R+ G     
Sbjct: 77  ELLRSAYEMLVERTEDLATLMTLEMGKPLAESRGEVAYGSEFFRWFSEEAVRISGRWSTA 136

Query: 170 SAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALA 229
                R + +KQPVG   +ITPWNFP AM TRK+G A+AAGCT+VVKPA +TP + L LA
Sbjct: 137 PNGATRLVTMKQPVGPTLMITPWNFPLAMGTRKIGPAIAAGCTMVVKPAAETPLTMLLLA 196

Query: 230 QLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSVK 289
           Q+  + G+P GV NVI  S +   +V E L  DP   K++FTGST  G+ L+  +A  + 
Sbjct: 197 QILEEVGLPKGVLNVITTSTSG--QVMEPLIRDPRSRKLTFTGSTPIGQKLIEQSAEQLL 254

Query: 290 RVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFA 349
           RVSMELGG APF+VF+ A++D AV GAM +K RN G+ C  +NRFLV   + D F  + A
Sbjct: 255 RVSMELGGNAPFLVFEDADLDAAVEGAMLAKMRNIGEACTAANRFLVHADVADEFSRRLA 314

Query: 350 EAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGGNFFE 409
           E M  +L VG+G ++ T  GPLIN KAV+KV+  V DA  +GA VVTGG+     G F+ 
Sbjct: 315 ERMG-ALTVGDGMDDDTKVGPLINAKAVDKVKALVEDAKGRGARVVTGGETVGDRGFFYA 373

Query: 410 PTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIWRV 469
           PT+L++VT +     EE FGPVA +  F  E +A+  AN+ + GL  YF+++D ++  RV
Sbjct: 374 PTVLTDVTGEADMAREEIFGPVAGIQTFTDEADAIERANSTEYGLVAYFFTKDFSRAIRV 433

Query: 470 AEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYV 518
           +E LE GMVGVN+G++S+   PFGGVK SG GREG   GIDEYLE KYV
Sbjct: 434 SEALEYGMVGVNQGIVSNPAAPFGGVKASGFGREGGFEGIDEYLETKYV 482


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: 615
Number of extensions: 31
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: 486
Length adjustment: 34
Effective length of query: 489
Effective length of database: 452
Effective search space:   221028
Effective search space used:   221028
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