Alignments for a candidate for acn in Sulfurivirga caldicuralii DSM 17737

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Sulfurivirga caldicuralii DSM 17737

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_074201305.1 BUQ81_RS05155 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_900141795.1:WP_074201305.1
          Length = 868

 Score = 1206 bits (3119), Expect = 0.0
 Identities = 593/853 (69%), Positives = 698/853 (81%), Gaps = 13/853 (1%)

Query: 2   LEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEAA 61
           L+ YR+HV ERA EG+ P PL+A Q A LVEL+KNPPAGEE FL+DLL NRVPPGVDEA+
Sbjct: 4   LQAYRQHVEERAKEGLPPLPLNAEQTAQLVELIKNPPAGEEAFLIDLLENRVPPGVDEAS 63

Query: 62  YVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALD--DAKLAPIAAKAL 119
           YVKA FLA +AKG   +PL+TPE+A  LLGTM GGYN+ PLI+ LD  +  +A  A  AL
Sbjct: 64  YVKAAFLADVAKGNVSTPLITPERATFLLGTMLGGYNVQPLIELLDSDNEAVAEEAVNAL 123

Query: 120 SHTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNT 179
             TLL++D ++DV++KA  GN  A++VMQ WADAEWF N+  L EKLTVTVFKV GETNT
Sbjct: 124 GKTLLVYDAYHDVKQKADQGNARAQEVMQRWADAEWFKNKDPLPEKLTVTVFKVDGETNT 183

Query: 180 DDLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDV 239
           DDLSPAP AWSRPDIPLHA  ML+     +E          ++I  ++ KG P+A+VGDV
Sbjct: 184 DDLSPAPAAWSRPDIPLHAKEMLRAKMPDVE----------EKIAEMKAKGHPVAFVGDV 233

Query: 240 VGTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVS 299
           VGTGSSRKSA NS++W  G DIP+VPNKR GG+ LGGKIAPIFFNT ED+GALPIE DV+
Sbjct: 234 VGTGSSRKSAMNSIMWHFGKDIPYVPNKRQGGVILGGKIAPIFFNTAEDSGALPIECDVT 293

Query: 300 NLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKARE 359
            + MGDVI +YPY+G++ N E GE+++TFELK   + DEVRAGGRIPLIIGRGLT +AR 
Sbjct: 294 KMQMGDVITIYPYEGKIEN-EAGEVISTFELKPVTMPDEVRAGGRIPLIIGRGLTDRARR 352

Query: 360 ALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGP 419
            +GL  SDVF + +D + S +G++LAQKMVG+ACG++G+RPG YCEP MT+VGSQDTTG 
Sbjct: 353 DMGLDVSDVFIRPRDESGSTKGYTLAQKMVGKACGIEGVRPGMYCEPHMTTVGSQDTTGA 412

Query: 420 MTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVI 479
           MTRDELK+LACLGFSAD V+QSFCHTAAYPKPVDV   H LPDFI++RGGVSLRPGDGVI
Sbjct: 413 MTRDELKELACLGFSADFVLQSFCHTAAYPKPVDVKLQHELPDFIISRGGVSLRPGDGVI 472

Query: 480 HSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGK 539
           HSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAA  GVMPL MPESVLVRFKG+
Sbjct: 473 HSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAATLGVMPLTMPESVLVRFKGE 532

Query: 540 MQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDAS 599
           MQPGITLRDLV+AIP  AI++GLLTVEKKGKKN+F+GR+LEIEGL +L VEQAFEL+DAS
Sbjct: 533 MQPGITLRDLVNAIPYVAIQKGLLTVEKKGKKNVFNGRVLEIEGLENLTVEQAFELSDAS 592

Query: 600 AERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLE 659
           AERSA GCT+KLNKEPIIE+L SNI L+ WMI  GY D RTL RR   M+ W+ NPELLE
Sbjct: 593 AERSANGCTVKLNKEPIIEFLKSNIALIDWMIENGYQDARTLARRRDAMKAWIENPELLE 652

Query: 660 ADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRA 719
           AD DAEYA VI+IDL +I EP+L  PNDPDD +PLS VQ   IDEVFIGSCMTNIGH+RA
Sbjct: 653 ADKDAEYAEVIEIDLNEITEPLLACPNDPDDIKPLSEVQNTSIDEVFIGSCMTNIGHYRA 712

Query: 720 AGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARV 779
           AGK+L+   GQLP RLW+APPT+MD  QL EEGYY++FG+ GAR E+PGCSLCMGNQARV
Sbjct: 713 AGKVLEKFNGQLPVRLWIAPPTKMDEHQLIEEGYYAIFGRVGARTEMPGCSLCMGNQARV 772

Query: 780 ADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVD 839
           ADGATV+STSTRNFPNR+G  ANVFL SAEL+A+ A++G+LPT EEY  Y+  ++  A +
Sbjct: 773 ADGATVMSTSTRNFPNRMGKDANVFLGSAELSAITAILGRLPTVEEYHQYMQDINAMAGE 832

Query: 840 TYRYLNFNQLSQY 852
            YRYL F++L +Y
Sbjct: 833 IYRYLQFDELPEY 845


Lambda     K      H
   0.317    0.136    0.400 

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: 2029
Number of extensions: 72
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: 865
Length of database: 868
Length adjustment: 42
Effective length of query: 823
Effective length of database: 826
Effective search space:   679798
Effective search space used:   679798
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 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 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