GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Sulfuritalea hydrogenivorans sk43H DSM 22779

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein

Query= SwissProt::Q9H2A2
         (487 letters)



>NCBI__GCF_000828635.1:WP_041097806.1
          Length = 479

 Score =  285 bits (730), Expect = 2e-81
 Identities = 164/474 (34%), Positives = 265/474 (55%), Gaps = 13/474 (2%)

Query: 13  FIDGKFLPCSSY--IDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERS 70
           +IDG+++  +    I+ + P+ G +   VP     + + AV AAR AF +WS     ER+
Sbjct: 8   YIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDAWSVTPAAERA 67

Query: 71  RVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQ 130
             L ++ + L+   +E A+  + + G     ++ + +     +F  ++        E   
Sbjct: 68  AYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADFPFE--- 124

Query: 131 MDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWML 190
            + +G     VR  VGV   I+PWN PL+ +  K+A A+AAG TV+ KPSE+  + A++L
Sbjct: 125 -EKVGNSK-VVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLNAFLL 182

Query: 191 CKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKL 250
            +++  AGVP GV N++ G GP VGEA+V+H EV ++SFTGS     R+++L++   K++
Sbjct: 183 AEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTRVSELASATVKRV 242

Query: 251 SLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVEA 310
           +LELGGK+ AII +DA+ +  +   V + + N G+ C   +R+ V  + Y+E  K  VEA
Sbjct: 243 ALELGGKSAAIILDDADFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEAAKLAVEA 302

Query: 311 TRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLP-ARNQA 369
            + ++VG P    V++G L SK   ++VR Y+ + +AEG ++  G G D   LP   N  
Sbjct: 303 AQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTG-GAD---LPEGVNPD 358

Query: 370 GYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVG 429
           GY++ PT+   +K +S    EEIFGPV  ++ +  EE+ +  AN   YGLA  VWS+   
Sbjct: 359 GYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSATDE 418

Query: 430 RVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTI 483
              +VA+++++G V  N      +  PFGG K SG GRE  K   + F E K +
Sbjct: 419 HAEQVARRMRTGQVEINGGTF-NMYAPFGGYKQSGNGRELGKYGLEDFLEFKAM 471


Lambda     K      H
   0.319    0.133    0.404 

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: 504
Number of extensions: 19
Number of successful extensions: 4
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: 487
Length of database: 479
Length adjustment: 34
Effective length of query: 453
Effective length of database: 445
Effective search space:   201585
Effective search space used:   201585
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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