GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Rhizobium etli CFN 42

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_008534338.1 RHE_RS29885 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_000092045.1:WP_008534338.1
          Length = 495

 Score =  522 bits (1344), Expect = e-152
 Identities = 262/481 (54%), Positives = 341/481 (70%), Gaps = 6/481 (1%)

Query: 46  LLRGDSFVGGRWLPTPAT---FPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKE 102
           L+R    VGG+W           V +P++   L ++   G+ E RA++ AA  A   W +
Sbjct: 16  LVREQMLVGGKWSSEGVNGTRINVLNPSTMDVLASLPSAGLAEVRASIDAAKAAQKKWAK 75

Query: 103 ISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRV 162
           +S KERS ++RK+Y+ ++ N ++LA I+T+E GKPL EA+GEI Y A ++EWF EEA+RV
Sbjct: 76  VSAKERSLIMRKFYEEVVANAEDLAVILTSEMGKPLAEARGEIAYGASYIEWFGEEAKRV 135

Query: 163 YGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTP 222
           YGD I     DKR LV+KQPVGV + I PWNFPSAM+ RK+  ALA+GC +V KPA +TP
Sbjct: 136 YGDTIPGHQADKRLLVIKQPVGVVAAIAPWNFPSAMVCRKIAPALASGCAIVFKPAAETP 195

Query: 223 YSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLH 282
            SALALA LA +AGIP G+++V+P     A+  GE +C++P+V K++FTGST  G+IL+ 
Sbjct: 196 LSALALAILAERAGIPDGLFSVLPTDN--ARMFGEEVCSNPVVKKLTFTGSTEVGRILMA 253

Query: 283 HAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHD 342
             A  + ++S+ELGG APFIVFD A++DQAV GAM SKFRNAGQTCVC+NR  VQ GIHD
Sbjct: 254 QGAQKIMKLSLELGGNAPFIVFDDADLDQAVEGAMLSKFRNAGQTCVCANRIYVQSGIHD 313

Query: 343 SFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQ 402
            FV K A  +  +L+V +GFE G T GPLIN++AV K+  H++DAV KGATVV GG R  
Sbjct: 314 RFVEKLAMRVS-ALQVLDGFESGATIGPLINDEAVAKLYGHIDDAVTKGATVVVGGDRDA 372

Query: 403 SGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQD 462
            GG F +PTLLS  T+DM    EETF P+APV KFD  EE + +AN  + GLA YF++ D
Sbjct: 373 RGGTFVQPTLLSGATKDMKVAREETFAPLAPVFKFDTVEEVIELANDTEFGLAAYFFAND 432

Query: 463 PAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGG 522
              +W+V E LE GMVGVN GLIS+   PFGGVKQSG GREGSKYG+D++L +KYVC GG
Sbjct: 433 LRNVWKVTEALEYGMVGVNTGLISTELAPFGGVKQSGFGREGSKYGMDDFLSMKYVCMGG 492

Query: 523 L 523
           +
Sbjct: 493 I 493


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: 652
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: 495
Length adjustment: 34
Effective length of query: 489
Effective length of database: 461
Effective search space:   225429
Effective search space used:   225429
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 Apr 09 2024. 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