GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Rhizobium etli CFN 42

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate WP_011425015.1 RHE_RS08800 aldehyde dehydrogenase family protein

Query= SwissProt::Q9H2A2
         (487 letters)



>NCBI__GCF_000092045.1:WP_011425015.1
          Length = 506

 Score =  319 bits (818), Expect = 1e-91
 Identities = 186/477 (38%), Positives = 275/477 (57%), Gaps = 14/477 (2%)

Query: 14  IDGKFLPCSSY-IDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPS--WSSRSPQERS 70
           IDGK+   +S+ I+   PS G    R P     + E A+ AAR+AF    W   +  ERS
Sbjct: 22  IDGKWEAGASHPIERIAPSHGVTVSRFPAGSATDAERAIAAARKAFDEGPWPRMTASERS 81

Query: 71  RVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSS--LHHTSEC 128
            +L + ADL+    EE A  ++ + GK +   R  +I  SV  +R+ A+ +  LH  S  
Sbjct: 82  AILLKAADLIAARAEELAFLDAIEAGKPITQVRG-EIAGSVDIWRYAAALARDLHGESYN 140

Query: 129 TQMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAW 188
           T  D  G +   +R  +GV  +I+PWN P  ++  K+  A+AAG T + KPSELTS +  
Sbjct: 141 TLGD--GTVGVVLREAIGVVSIITPWNFPFLIVGQKLPFALAAGCTTVVKPSELTSGSTL 198

Query: 189 MLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCK 248
           +L ++L +AGVP GVVNIV GTGP VG  + SHP+V +ISFTGS    +   + +A   K
Sbjct: 199 VLGEILQQAGVPDGVVNIVTGTGPEVGAVMTSHPDVDMISFTGSTGVGKLTMKNAAQTLK 258

Query: 249 KLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFV 308
           K+SLELGGKNP I+F DA+LD  I A V  ++ N GE C   SR+ + KSI S+ ++R  
Sbjct: 259 KVSLELGGKNPQIVFPDADLDAFIDAAVFGAYFNAGECCNAGSRLILHKSIASDVVRRVA 318

Query: 309 EATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARNQ 368
           E ++  KVG P DP   +GA+I+  HLEK+  YV  A + GA++  G     L +     
Sbjct: 319 ELSKGVKVGDPLDPQTQVGAIITPQHLEKISGYVAGARSNGARVTHGGETLDLGM----- 373

Query: 369 AGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNV 428
            G FM PT++  +  +     EE+FGPV  V+ F++  E +  AN++ YGL+A VWS + 
Sbjct: 374 -GQFMSPTILEAVTPDMAVAREEVFGPVLSVLTFETTAEAVRIANSIDYGLSAGVWSRDF 432

Query: 429 GRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITV 485
                + + +++G +W N ++     LPFGG K SG+GRE  + + + +TE KT+ +
Sbjct: 433 DTCLTIGRSVRAGTIWMNTFMDGASELPFGGYKQSGLGRELGRHAVEDYTETKTLNM 489


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: 554
Number of extensions: 18
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: 506
Length adjustment: 34
Effective length of query: 453
Effective length of database: 472
Effective search space:   213816
Effective search space used:   213816
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