GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Novosphingobium fuchskuhlense FNE08-7

Align Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; P5C dehydrogenase; Aldehyde dehydrogenase family 4 member A1; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_067912849.1 AQZ52_RS15205 aldehyde dehydrogenase family protein

Query= SwissProt::Q8CHT0
         (562 letters)



>NCBI__GCF_001519075.1:WP_067912849.1
          Length = 474

 Score =  120 bits (302), Expect = 9e-32
 Identities = 106/359 (29%), Positives = 166/359 (46%), Gaps = 22/359 (6%)

Query: 179 LEGEQPISVPPSTNHTVYRGLEGFVAAISPFNFTAIGGNLAGAPALM-GNVVLWKPSDTA 237
           LEG +  +  P  N        G VAAI+P+N+         AP +  GN V+ KPS+  
Sbjct: 118 LEGFEWEAPVPGANARFVHEPIGVVAAITPWNWPLNQICAKIAPCIAAGNTVVLKPSEEC 177

Query: 238 MLASYAVYRILREAGLPPNIIQFVPADGPTFGDTVTSSEHLCGINFTGSVPTFKHLWRQV 297
              +  +  ++  AG+P  +   V  DGP  G  +T    +  ++FTGS      + +  
Sbjct: 178 PSNAVIMAEVMHAAGVPAGVFNLVQGDGPGVGVALTVHPDVDMVSFTGSTRAGIQIAKNA 237

Query: 298 AQNLDRFRTFPRLAGECGGKNFHFVHSSADVDSVVSGTLRSAFEYGGQKCSACSRLYVPK 357
           A       T  R+  E GGK+ + V   AD  + + GTL+      GQ C A +R+ VPK
Sbjct: 238 AD------TVKRVHQELGGKSPNLVLEDADFAATLPGTLQGIVANTGQSCIAPTRILVPK 291

Query: 358 SLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVIDAKAFARIKKWLEHARSSPSLSILAG 417
           S   + +  +    + +KVG P E+ G     V++   +++++  ++    +   S+L G
Sbjct: 292 SRKEEAETFVKNYFAAVKVGSPEEE-GMHIGPVVNKAQWSKVQSLID-TSIAEGASLLEG 349

Query: 418 G---QCNESVGYYVEPCIIESKDPQEPIMKEEIFGPVLTVYVYPDDKYRETLQLVDSTTS 474
           G     N + GYY+ P +     P   I +EE FGPV T+  Y  D   + ++L  + T+
Sbjct: 350 GPGLPDNVNRGYYIRPTVFSDVTPDMTIFREETFGPVATITTY--DGIEDGIELA-NRTA 406

Query: 475 YGLTGAVFAQDKAIVQEATRMLRNAAGNFYINDKSTGSVVGQQPFGGARASGTNDKPGG 533
           YGL+ AV   D    +     LR  AG   +N    G V G   FGG + SG N + GG
Sbjct: 407 YGLS-AVVTGDVETAKGIVGRLR--AGLVAVN--QWGGVKG-GAFGGYKQSG-NGREGG 458


Lambda     K      H
   0.319    0.135    0.411 

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: 606
Number of extensions: 27
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: 562
Length of database: 474
Length adjustment: 35
Effective length of query: 527
Effective length of database: 439
Effective search space:   231353
Effective search space used:   231353
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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