Alignments for a candidate for acn in Sulfuricurvum kujiense DSM 16994

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Sulfuricurvum kujiense DSM 16994

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_013460045.1 SULKU_RS05970 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>NCBI__GCF_000183725.1:WP_013460045.1
          Length = 869

 Score = 1045 bits (2701), Expect = 0.0
 Identities = 532/869 (61%), Positives = 656/869 (75%), Gaps = 26/869 (2%)

Query: 2   LEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEAA 61
           ++EY+ HVAER AQGI P PL   Q+ ALVEL+ T    +   L+++L  RV PGVD+ A
Sbjct: 4   MDEYKAHVAEREAQGIPPLPLTKEQVTALVELI-TAESSKNAELVEMLAERVNPGVDDGA 62

Query: 62  YVKAGFLAAVAKGDTTSPLVS---------PEKAIELLGTMQGGYNIHPLIDALDDAKLA 112
           +VKA FL  V +G   + L            + AI++LG M GGYN+ PLIDAL +  +A
Sbjct: 63  HVKAAFLHQVVQGQVKAFLADNSDINSDDHKKAAIKILGKMVGGYNVKPLIDALSNDAIA 122

Query: 113 PIAAKALSHTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFK 172
             AA  L HTLL++D F D+ + ++  N+YAK+V+QSWADAEWF ++ PLAEK +V VFK
Sbjct: 123 NEAAHELKHTLLVYDAFNDIVDLSQT-NKYAKEVLQSWADAEWFTAKKPLAEKFSVVVFK 181

Query: 173 VTGETNTDDLSPAPDAWSRPDIPLHAQAMLK-NAREGIEPDQPGVVGPIKQIEALQKKGY 231
             GETNTDDLSPA  A++R DIPLHA  ML     EGI            +I  L+K G 
Sbjct: 182 FPGETNTDDLSPASAAFTRSDIPLHATTMLSAKMPEGIA-----------KIAELKKMGK 230

Query: 232 PLAYVGDVVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGA 291
            +AYVGDVVGTGSSRKSA NSV W MGDDIP +PNKR GG+ +G  IAPIFF T ED+GA
Sbjct: 231 QIAYVGDVVGTGSSRKSAANSVQWHMGDDIPGIPNKRTGGVVIGSIIAPIFFATCEDSGA 290

Query: 292 LPIEVDVSNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGR 351
           LPIE DVS +  GDV+D+    G +  +  G  +ATF L+ + + DEVRAGGRIPLIIGR
Sbjct: 291 LPIEADVSQMETGDVLDIDTKAGTITKN--GTQIATFSLRPNTIEDEVRAGGRIPLIIGR 348

Query: 352 GLTTKAREALGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSV 411
           GLT KAR ALG+  + +F      A++ +G++LAQKMVG+ACG++G+RPG YCEP  ++V
Sbjct: 349 GLTAKARAALGMAPATIFATPIQPADTGKGYTLAQKMVGKACGMEGVRPGMYCEPMTSTV 408

Query: 412 GSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVS 471
           GSQDTTGPMTRDE+K+L+ LGFSAD V+QSFCHTAAYPKP DV  H TLP FI +R GV+
Sbjct: 409 GSQDTTGPMTRDEIKELSALGFSADFVLQSFCHTAAYPKPSDVKLHATLPAFISSRSGVA 468

Query: 472 LRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPES 531
           LRP DGVIHSWLNRM+LPDTVGTGGDSHTRFPIG+SFPAGSGLVAFAA TG MPL+MPES
Sbjct: 469 LRPADGVIHSWLNRMVLPDTVGTGGDSHTRFPIGVSFPAGSGLVAFAAVTGSMPLEMPES 528

Query: 532 VLVRFKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQ 591
           VLVRFKG+MQPGITLRDLV+AIP YAIKQGLLTVEKKGKKNIF+GR+LEIEGLP++KVEQ
Sbjct: 529 VLVRFKGEMQPGITLRDLVNAIPYYAIKQGLLTVEKKGKKNIFNGRVLEIEGLPNMKVEQ 588

Query: 592 AFELTDASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKW 651
           AFEL+DASAERSAA CT++LNKEP++EYL SN+ L++ MI +GY D RTL+RR   M++W
Sbjct: 589 AFELSDASAERSAAACTVRLNKEPVIEYLKSNVTLIEAMIKDGYEDARTLQRRADKMKEW 648

Query: 652 LADPQLLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCM 711
           LA P L+E DADAEYAA+I+IDL ++KEPIL  PNDPD+ +LLS+V GEKIDEVF+GSCM
Sbjct: 649 LAAPSLMEPDADAEYAAIIEIDLNEVKEPILACPNDPDNVKLLSEVAGEKIDEVFLGSCM 708

Query: 712 TNIGHFRAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSL 771
           TNIGH+RAAG+++         + W+ PPTRMD  QL  EGYY V+    A+ E+PGCSL
Sbjct: 709 TNIGHYRAAGEVMRGEGKIAVEKFWIVPPTRMDEQQLINEGYYDVYKAIAAQTEVPGCSL 768

Query: 772 CMGNQARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVA 831
           CMGNQA   +G+TV STSTRNF NRLG G  V+L SAELAAV A +G++PT  EY + V 
Sbjct: 769 CMGNQASSREGSTVFSTSTRNFDNRLGKGTQVYLGSAELAAVCAKLGRIPTVAEYMSIVP 828

Query: 832 Q-VDKTAVDTYRYLNFDQLSQYTEKADGV 859
           + +   A D Y+YLNF++++ Y+ +A  V
Sbjct: 829 EKLAGKADDVYKYLNFNEIASYSLQARNV 857


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: 1910
Number of extensions: 68
Number of successful extensions: 7
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: 869
Length adjustment: 42
Effective length of query: 823
Effective length of database: 827
Effective search space:   680621
Effective search space used:   680621
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 Apr 09 2024. 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 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