GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Methylocystis bryophila S285

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein

Query= BRENDA::Q88RC0
         (480 letters)



>NCBI__GCF_002117405.1:WP_085772038.1
          Length = 506

 Score =  273 bits (697), Expect = 1e-77
 Identities = 178/491 (36%), Positives = 250/491 (50%), Gaps = 32/491 (6%)

Query: 10  RQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTA 69
           R   +I G+W+    G+     +P TG  I  V +   A+   A++AA KA  AW    A
Sbjct: 18  RYDNFIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKAKDAWGKTPA 77

Query: 70  KERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKG-EIAYAASFIEWFAE------- 121
            ER+  L +  + + +N   LA + T + GKP+ E    +I  A     +FA        
Sbjct: 78  AERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQEG 137

Query: 122 EAKRIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKP 181
               I  DT+  H          +P+GV   I PWNFP  M   K  PALAAG  +VLKP
Sbjct: 138 SLSEIDHDTVAYH--------FHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKP 189

Query: 182 ASQTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQL 241
           A QTP S LA+ EL     +P GVL++V G   E G  L  N  + K++FTG T  GR +
Sbjct: 190 AEQTPMSILAVAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLI 248

Query: 242 MEECAKDIKKVSLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRI 295
           M+  A+++  V+LELGG +P I F      DDA LDKA+EG   S   N G+ C C +R 
Sbjct: 249 MQYAAENLIPVTLELGGKSPNIFFADVMAEDDAFLDKALEG-FASFALNQGEVCTCPSRA 307

Query: 296 YVQDGVYDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVL 355
            VQ  +YD F EK  A VAK++ G+ L+  T  G       + K+  +++    +GAKVL
Sbjct: 308 LVQRSIYDKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVL 367

Query: 356 SG-------GKLIEGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDT 408
            G       G+L EG + +PT L +      V +EE FGP+  +  F+ E E + ++NDT
Sbjct: 368 IGGERSVLEGELKEGYYMQPTAL-EGHNRMRVFQEEIFGPVVSVTTFETEEEALQIANDT 426

Query: 409 EFGLASYFYARDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIE 468
            +GL +  + RD SR +R   A+  G V  N        A FGG K SG+GRE  K  ++
Sbjct: 427 LYGLGAGLWTRDGSRAYRCGRAIRAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLD 486

Query: 469 DYLEIKYLCIS 479
            Y + K L +S
Sbjct: 487 HYQQTKNLLVS 497


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: 552
Number of extensions: 34
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: 506
Length adjustment: 34
Effective length of query: 446
Effective length of database: 472
Effective search space:   210512
Effective search space used:   210512
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 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