Alignments for a candidate for fumD in Desulfatiglans anilini DSM 4660

GapMind for catabolism of small carbon sources

Alignments for a candidate for fumD in Desulfatiglans anilini DSM 4660

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate WP_028319820.1 H567_RS0100100 fumarate hydratase

Query= BRENDA::Q141Z6
         (520 letters)



>NCBI__GCF_000422285.1:WP_028319820.1
          Length = 279

 Score =  181 bits (459), Expect = 3e-50
 Identities = 107/290 (36%), Positives = 163/290 (56%), Gaps = 14/290 (4%)

Query: 14  MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 73
           M  I+ + + +++  ++   +Y    D IQ+  +A   E+SP  ++ + +++ N+R+   
Sbjct: 1   MRHIEAQAVTEAVKAAVVKANYELGEDVIQSFEKARIDEESPVGREILERLIENARIART 60

Query: 74  GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG 133
            + PICQDTG+V VF  VG +V       G  + + +GVR GY   +  LR S+  P   
Sbjct: 61  ERIPICQDTGLVVVFADVGQEVVVSNG--GFAEAVEQGVRDGY--EEGYLRKSVCHPFT- 115

Query: 134 GRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPS---DSIVDWILKTV 190
            RKNT DNTP +IH+ +V G+ + + V  KGGGSEN S+  ML PS     + + I+ TV
Sbjct: 116 -RKNTGDNTPVIIHFNLVKGSGIRMWVVPKGGGSENMSRLFMLPPSAGWTGVKEKIVLTV 174

Query: 191 PTMGAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEK 250
              G   CPP ++G+GIGG  E++ +MAK SL+ P+   +     P D +  +  E+ E 
Sbjct: 175 EEAGPNPCPPTIVGVGIGGNFEQSALMAKRSLLRPLGEPN-----PDDELARMEQEVLEA 229

Query: 251 VNALGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTL 300
           +N  G+G QGLGG  T L V I+  P H AS P+A+   C A+RH   TL
Sbjct: 230 INRTGVGPQGLGGRITSLAVHILMMPCHIASLPLAVNIQCHASRHLEVTL 279


Lambda     K      H
   0.316    0.133    0.392 

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: 337
Number of extensions: 16
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: 520
Length of database: 279
Length adjustment: 30
Effective length of query: 490
Effective length of database: 249
Effective search space:   122010
Effective search space used:   122010
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: 50 (23.9 bits)

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate WP_028319821.1 H567_RS0100105 Fe-S-containing hydro-lyase

Query= BRENDA::Q141Z6
         (520 letters)



>NCBI__GCF_000422285.1:WP_028319821.1
          Length = 185

 Score =  142 bits (357), Expect = 1e-38
 Identities = 73/174 (41%), Positives = 108/174 (62%), Gaps = 1/174 (0%)

Query: 336 LTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAKGEKLPVDFTNRVIYYVGPVDPV 395
           LT  +VAA   G  ++LSG + T RDAAH+R+ D++   E LP+  T +V+YYVGP    
Sbjct: 11  LTASDVAALRAGDRVILSGVLYTARDAAHRRLIDLIEAKEPLPIPLTGQVLYYVGPSPAP 70

Query: 396 RDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAERGPVAIEAIRKHKAAYLMAVGGA 455
               +G AGPTT+ RMD +T  +L + GL  +IGK +R     +A+  + A Y  A+GGA
Sbjct: 71  PGRPIGAAGPTTSYRMDPYTPQLL-EKGLKGIIGKGKRSEAVKQALMTYGAVYFAAIGGA 129

Query: 456 AYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAVDSNGTSVHQTGPKEWQ 509
             L+S++IR A V+A+ DLG EAI E  V+ MP+ V  D+ G  +++ G K ++
Sbjct: 130 GALMSQSIRKATVVAYHDLGPEAIRELYVEGMPLVVVNDTEGNDLYEEGRKAYR 183


Lambda     K      H
   0.316    0.133    0.392 

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: 235
Number of extensions: 8
Number of successful extensions: 2
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: 520
Length of database: 185
Length adjustment: 27
Effective length of query: 493
Effective length of database: 158
Effective search space:    77894
Effective search space used:    77894
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: 48 (23.1 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources