GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Verminephrobacter eiseniae EF01-2

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_041950131.1 VEIS_RS17310 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-11560
         (497 letters)



>NCBI__GCF_000015565.1:WP_041950131.1
          Length = 496

 Score =  365 bits (937), Expect = e-105
 Identities = 200/480 (41%), Positives = 288/480 (60%), Gaps = 6/480 (1%)

Query: 19  EGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQL 78
           +GR  I+G++ DA      E  SP  G+ +A  A   + DA RA+  AR  F+ G W  L
Sbjct: 11  QGRLLIDGQWCDAADARRLERRSPAHGQLVAVYAEAGVPDAQRAIGAARQAFDKGPWPLL 70

Query: 79  APAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKV 138
             A+R   L   AD +      LA +E+L+ GKP+  S + +I GAA    + A     +
Sbjct: 71  KGAERARILRHVADGILARRHALARMESLENGKPLAQSLA-EIEGAADLWQYAASLARNL 129

Query: 139 Y-DEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSP 197
           + D         L LV REP+GVVG I PWNFP L+   KL  ALA G + V+KP+E + 
Sbjct: 130 HGDSYNTLGAATLALVLREPIGVVGIITPWNFPFLIVSQKLPFALAAGCTAVVKPAEVTS 189

Query: 198 LTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAG 257
            T + + ++ +EAGIPAGV+N+L G G  VG+A+  H DVD L FTGST + KQ +  + 
Sbjct: 190 GTTVMLGEILLEAGIPAGVVNILVGQGAVVGEAMVSHPDVDMLSFTGSTAVGKQAVARSA 249

Query: 258 ESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317
            + +K++ LE GGK+P IVFAD  D +AA +AA   I FN G+ C +GSR+LV+ ++ DK
Sbjct: 250 -ATLKKVALELGGKNPQIVFADC-DWEAAVDAAVYGIFFNAGQCCNSGSRILVQDAVADK 307

Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377
           F   V+   +  + G+P D +T VGA+   +Q++T+L+++E   + GA +  GG R   +
Sbjct: 308 FAEAVIARSRQVRVGDPFDERTQVGAITTERQLHTILAHVEGARQAGATVALGGARL--D 365

Query: 378 TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSD 437
             G Y+EPT+  GVT  M IA++E+FGPVLS++ F T +EAV +AN T YGL+A +W+ D
Sbjct: 366 RPGLYMEPTVLTGVTRDMAIARQEVFGPVLSMLRFGTLDEAVDLANSTLYGLSAAVWSQD 425

Query: 438 ISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497
           I+     AR + AG+VWVN +  G    PFGG+++SG GR+    A E YTE K   + L
Sbjct: 426 INTCITAARRIEAGTVWVNTFLEGHAELPFGGYRESGIGRELGRFAAEDYTETKTVHLHL 485


Lambda     K      H
   0.316    0.132    0.390 

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: 593
Number of extensions: 20
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 497
Length of database: 496
Length adjustment: 34
Effective length of query: 463
Effective length of database: 462
Effective search space:   213906
Effective search space used:   213906
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 (21.6 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