Alignments for a candidate for acn in Thiothrix lacustris DSM 21227

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Thiothrix lacustris DSM 21227

Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_028487955.1 Q394_RS0102890 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>NCBI__GCF_000621325.1:WP_028487955.1
          Length = 867

 Score = 1345 bits (3480), Expect = 0.0
 Identities = 653/860 (75%), Positives = 751/860 (87%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           ML+EYR+HVAERAAQGI PKPLDA Q AALV+LLK PP GEE FL+DLL NRVP GVDEA
Sbjct: 1   MLQEYRQHVAERAAQGIPPKPLDAAQTAALVDLLKNPPKGEEAFLVDLLENRVPAGVDEA 60

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFLAAVA G+    L+S  +A+E+LG M GGYN+ PLI ALD    A +AA ALS
Sbjct: 61  AYVKAGFLAAVASGEVKCALISQVRAVEVLGMMLGGYNVQPLIAALDSEVTAAVAATALS 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
           HTLL+FD F+DVEEKAKAGN  AKQVM SWA  EWF S+P +A+KITVTVFKVTGETNTD
Sbjct: 121 HTLLVFDAFHDVEEKAKAGNAAAKQVMASWAAGEWFTSKPEVAKKITVTVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHA AMLK AR+GIEP+ PG VGP+KQIEA++ +G+P+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHANAMLKMARDGIEPEVPGSVGPLKQIEAMKAQGFPVAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDD+P +PNKR GG C G KIAPIFFNTMED+G+LPIE+DV+ 
Sbjct: 241 GTGSSRKSATNSVLWFFGDDMPGIPNKRVGGYCFGSKIAPIFFNTMEDSGSLPIEMDVAQ 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           +NMGDV+DVYPY+G  + H T E+++TF LKT VL+DE RAGGRI LIIGRGLT KARE+
Sbjct: 301 MNMGDVVDVYPYEGVAKRHGTDEVISTFGLKTQVLLDEARAGGRINLIIGRGLTAKARES 360

Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGLP  D+FR  +  A++ +GF+LAQKMVG+ACG+ G+RPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLPPVDLFRTPEQPADTGKGFTLAQKMVGKACGMTGVRPGMYCEPKMTTVGSQDTTGPM 420

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIM RGGVSLRPGDG+IH
Sbjct: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMTRGGVSLRPGDGIIH 480

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVRF GKM
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESVLVRFTGKM 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPGITLRDLVHAIP  AI+ GLLTVEKKGKKN+F+G ++EIEGL  L VEQAFEL+DASA
Sbjct: 541 QPGITLRDLVHAIPHKAIQMGLLTVEKKGKKNVFNGTVVEIEGLDHLTVEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQLLEA 660
           ERSAAGCT+ L++  + EYL SNIV+LKWM++EGYGD RT+ERRI  ME+WLA+P LL A
Sbjct: 601 ERSAAGCTVALSEASVAEYLRSNIVMLKWMLSEGYGDVRTIERRIGKMEEWLANPSLLRA 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFRAA 720
           DADAEYAAVI+I++ +IKEPILCAPNDPDDARLLS+V G KIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DADAEYAAVIEINMDEIKEPILCAPNDPDDARLLSEVAGRKIDEVFIGSCMTNIGHFRAA 720

Query: 721 GKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           GKLLD    Q+PTR+W+APPT+MDAAQL++EGYY+++G++GAR+E+PGCSLCMGNQAR+A
Sbjct: 721 GKLLDAANTQIPTRMWIAPPTKMDAAQLSDEGYYNIYGRAGARMEMPGCSLCMGNQARIA 780

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
           + +T VSTSTRNFPNRLGTGA+VFLASAELA+VAA++GKLPT  EY  Y  ++D  + D 
Sbjct: 781 EKSTAVSTSTRNFPNRLGTGADVFLASAELASVAAVMGKLPTVAEYMEYANKLDSMSADI 840

Query: 841 YRYLNFDQLSQYTEKADGVI 860
           YRYLNFD++  Y   A  V+
Sbjct: 841 YRYLNFDKMESYQHAAAKVV 860


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: 2131
Number of extensions: 74
Number of successful extensions: 1
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: 867
Length adjustment: 42
Effective length of query: 823
Effective length of database: 825
Effective search space:   678975
Effective search space used:   678975
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.

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

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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 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