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_157063607.1 VV02_RS11195 aldehyde dehydrogenase family protein

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_001190945.1:WP_157063607.1
          Length = 486

 Score =  422 bits (1086), Expect = e-122
 Identities = 228/480 (47%), Positives = 305/480 (63%), Gaps = 10/480 (2%)

Query: 41  DLHADLLRGDSFVGGRW--LPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFS 98
           D+H +LL     +GG+W    + ATF V DP++GA L  VAD    + + A+ AA +A +
Sbjct: 11  DVHKELL-----IGGQWSAADSDATFEVLDPSTGAVLAEVADASPADGQRALDAAVEAQA 65

Query: 99  SWKEISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEE 158
           ++   + +ER  +L K Y L+ +  D+LA ++T E GKPL EA+GEI Y+A F   F+ E
Sbjct: 66  AFAATTPRERYDILMKAYGLLHERIDDLALLMTLEMGKPLAEAKGEITYAAEFFRHFAFE 125

Query: 159 ARRVYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPA 218
           A R+ G      A   R L+ KQPVG   +ITPWNFP AM TRK+G A+AAGCT V+KPA
Sbjct: 126 ALRIDGGYQTAPAGGARFLISKQPVGPCLLITPWNFPMAMGTRKIGPAIAAGCTSVIKPA 185

Query: 219 EDTPYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGK 278
             TP S LAL  +  +AG+P GV N++ C    A +V E L       K+SFTGST  GK
Sbjct: 186 HQTPLSMLALGAILTEAGVPDGVVNIVTC--MNAGDVMEPLIKSGKARKLSFTGSTKVGK 243

Query: 279 ILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQR 338
           +LL   A+ V R SMELGG APFIVF+ A++D+AV GAMA+K RN G+ C  +NR  V  
Sbjct: 244 VLLEQCADKVLRTSMELGGNAPFIVFEDADMDEAVKGAMAAKMRNMGEACTAANRIFVHE 303

Query: 339 GIHDSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGG 398
            + D F  + ++AM + L+VG G E+G   GPLI+E   +KV   + DA A+GATV+TGG
Sbjct: 304 NVIDEFGKRLSQAMSE-LKVGRGTEDGVQVGPLIDEAGRQKVIDLLEDATARGATVLTGG 362

Query: 399 KRHQSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYF 458
                 G FF PT+L+ V  D    +EE FGPVAP+  F  E+E VA AN    GL  Y 
Sbjct: 363 DAPDGDGFFFTPTVLTGVPHDARMTSEEIFGPVAPLTPFTTEKEVVAAANDTPYGLVSYV 422

Query: 459 YSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYV 518
           ++ D  +  RVAE +E GMVG+N+G++S+   PFGG+K+SGLGREG   GIDE+LEVKY+
Sbjct: 423 FTNDLRRALRVAEAIESGMVGLNQGVVSNPAAPFGGIKESGLGREGGSVGIDEFLEVKYI 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: 649
Number of extensions: 24
Number of successful extensions: 3
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