GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Echinicola vietnamensis KMM 6221, DSM 17526

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::Q88RC0
         (480 letters)



>FitnessBrowser__Cola:Echvi_0481
          Length = 509

 Score =  271 bits (692), Expect = 5e-77
 Identities = 168/480 (35%), Positives = 257/480 (53%), Gaps = 18/480 (3%)

Query: 14  YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73
           +I G+++   +G+   V +P  G+V   V +   A+   A++AA KA PAW   +A ERS
Sbjct: 25  FIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPAWSRTSATERS 84

Query: 74  AKLRRWFELMIENQDDLARLMTTEQGKPLAEA-KGEIAYAASFIEWFAEEAKRIYGDTIP 132
             L +  + +    + LA + T + GKP+ E    ++A       +FA   +   G    
Sbjct: 85  NILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEGSIAE 144

Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALAL 192
             Q     + +K+PIG+   I PWNFP  M T K  PALAAGC  ++KPA QTP S + L
Sbjct: 145 LDQHTVS-VNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTPASIMIL 203

Query: 193 VELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKV 252
           +E+     +PAGVL+VV G   E G  L  +  + K++FTG T  GR +M+  ++++  V
Sbjct: 204 MEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQYASENLNPV 262

Query: 253 SLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFA 306
           ++ELGG +P + F      DD  LDK +EGA++    N G+ C C +RI V + +YDAF 
Sbjct: 263 TMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFAL-NQGEVCTCPSRILVHEKIYDAFM 321

Query: 307 EKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGK------- 359
           EK+ A    +++G+ L++ T  G         K+  +I+    +GA+VL+GG+       
Sbjct: 322 EKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGGEVAKLNSG 381

Query: 360 LIEGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYAR 419
           L  G + +PT+L    K   V +EE FGP+  +  FKD  E I++SNDT +GL +  + R
Sbjct: 382 LENGYYVKPTLLKGHNK-MRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGLGAGVWTR 440

Query: 420 DMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCIS 479
           D    ++V  A++ G V +N        APFGG K SG GRE     +  Y + K + IS
Sbjct: 441 DAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYRQNKNMLIS 500


Lambda     K      H
   0.317    0.134    0.384 

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: 553
Number of extensions: 26
Number of successful extensions: 7
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: 480
Length of database: 509
Length adjustment: 34
Effective length of query: 446
Effective length of database: 475
Effective search space:   211850
Effective search space used:   211850
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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