GapMind for catabolism of small carbon sources

 

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

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__Cola:Echvi_0481
          Length = 509

 Score =  322 bits (826), Expect = 1e-92
 Identities = 184/483 (38%), Positives = 275/483 (56%), Gaps = 16/483 (3%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           FI G++    + E F+ + PV      K+ARGK+ DI+ A+ AA   F    WS +S  +
Sbjct: 25  FIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPA--WSRTSATE 82

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R  +L K+AD +E   E LA +ET+D GKP+R ++  D+       R++A  I    G +
Sbjct: 83  RSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEGSI 142

Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202
           A    H +++ V+EP+G++  I+PWNFP+L+  WK+ PALAAG   I+KP+E++P S + 
Sbjct: 143 AELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTPASIMI 202

Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262
           L  +  +  LP GVLNVV GFG EAG+ L++   +D +AFTG T TG+ +++ A + N+ 
Sbjct: 203 LMEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQYASE-NLN 260

Query: 263 RVWLEAGGKSANIVFADCPDLQ----QAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318
            V +E GGKS N+ F    D            A     NQG+VC   +R+L+ E I D F
Sbjct: 261 PVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFALNQGEVCTCPSRILVHEKIYDAF 320

Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG-----RNA 373
           +  +  +A+  Q GHPLD  T MG        + + S+I  G+ +G  +L G      N+
Sbjct: 321 MEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGGEVAKLNS 380

Query: 374 GLAAA--IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431
           GL     + PT+    +    + +EEIFGPV  V  F   E+A+ ++ND+ YGLGA VWT
Sbjct: 381 GLENGYYVKPTLLKGHN-KMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGLGAGVWT 439

Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491
           RD   A+++ R +KAG V+VN Y+      PFGGYK+SG GR+  L  L  + + K + I
Sbjct: 440 RDAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYRQNKNMLI 499

Query: 492 SLE 494
           S +
Sbjct: 500 SYD 502


Lambda     K      H
   0.317    0.133    0.389 

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: 559
Number of extensions: 23
Number of successful extensions: 5
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: 495
Length of database: 509
Length adjustment: 34
Effective length of query: 461
Effective length of database: 475
Effective search space:   218975
Effective search space used:   218975
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 17 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