GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Methylocapsa aurea KYG

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein

Query= BRENDA::Q88RC0
         (480 letters)



>NCBI__GCF_000746085.1:WP_036262823.1
          Length = 506

 Score =  276 bits (705), Expect = 2e-78
 Identities = 174/487 (35%), Positives = 256/487 (52%), Gaps = 32/487 (6%)

Query: 14  YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73
           +I G+W+ A  GQT +  +P  G VI TV +    +   A++AA  A  AW   +  ERS
Sbjct: 22  FIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAARGAWGRTSPAERS 81

Query: 74  AKLRRWFELMIENQDDLARLMTTEQGKPLAEAKG-EIAYAASFIEWFAEEAKRIYG---- 128
             L R  + + +  D LA + T + GKP+ E K  ++  A     +FA   +   G    
Sbjct: 82  LALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEGGISE 141

Query: 129 ---DTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQT 185
              DT+  H          +P+GV A I PWNFP  M   K  PALAAG  ++LKPA QT
Sbjct: 142 IDHDTVAYH--------FHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQT 193

Query: 186 PYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEEC 245
           P S + LV++     +P GVL+V+ G   E G  L  N  + K++FTG T  GR +M+  
Sbjct: 194 PMSVMVLVDMIGDL-LPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGRLIMQYA 252

Query: 246 AKDIKKVSLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRIYVQD 299
           +++I  V+LELGG +P I F      DD   DKA+EG  +    N G+ C C +R  VQ+
Sbjct: 253 SENIIPVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFAL-NQGEVCTCPSRALVQE 311

Query: 300 GVYDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGG- 358
            +YD F E+  A V K+K GN L+  T  G       + K+  +++    +GAKVL+GG 
Sbjct: 312 KIYDRFMERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGGG 371

Query: 359 ------KLIEGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGL 412
                 +L  G + +PTIL    K   + +EE FGP+  +  FKD+ E + ++NDT +GL
Sbjct: 372 RADVGPELAGGFYVQPTILEGHNKMR-IFQEEIFGPVLSVTSFKDDEEALEIANDTLYGL 430

Query: 413 ASYFYARDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLE 472
            +  + R+ +R +R   A+E G V  N   +    A FGG K SG+GRE  K  ++ Y +
Sbjct: 431 GAGVWTRNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQK 490

Query: 473 IKYLCIS 479
            K + +S
Sbjct: 491 TKNMLVS 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: 556
Number of extensions: 29
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: 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