Alignments for a candidate for acn in Geotalea uraniireducens Rf4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Geotalea uraniireducens Rf4

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_011938832.1 GURA_RS09830 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>NCBI__GCF_000016745.1:WP_011938832.1
          Length = 843

 Score = 1024 bits (2647), Expect = 0.0
 Identities = 528/854 (61%), Positives = 641/854 (75%), Gaps = 14/854 (1%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           M+E Y K  AER A GI  KPLD  Q A L +LL+ PP G+E FLL+LL  RV PGVD A
Sbjct: 1   MIEAYLKQEAERQAMGIPAKPLDPEQTADLCKLLENPPAGKESFLLNLLKERVSPGVDPA 60

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A VKA FLA +  G  TSPLVS ++A+++LGTM GGYN+ PL++AL DA LA  AAKALS
Sbjct: 61  AEVKAAFLAKIVNGAATSPLVSKKEAVQILGTMLGGYNVTPLVEALKDAALAEDAAKALS 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
              L++D F +V   +K  N  AK+V++SWA+AEWF S+P +   I V V+KV GE NTD
Sbjct: 121 GITLVYDAFDEVLALSKT-NASAKKVVESWANAEWFTSKPGVPATIKVKVYKVEGEINTD 179

Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
           D SPA DAWSRPDIPLH+ AM K       PD       +  I   +  G+ +A+ GDVV
Sbjct: 180 DFSPAGDAWSRPDIPLHSLAMGKTRF----PDG------LATIAKYRADGFQVAFAGDVV 229

Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSA NSVLW  G+DIP VPNKR GG+ +GG IAPIFFNT +D+GALP++ DV+ 
Sbjct: 230 GTGSSRKSACNSVLWANGNDIPCVPNKRRGGVIIGGVIAPIFFNTAQDSGALPLKADVTK 289

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           +N GDVI +   KGE+++ E GELL+TF++  + L DE +AGGRIPLIIGR LT +AR A
Sbjct: 290 MNTGDVIIIDTVKGEIKS-EGGELLSTFKINPNTLADEFQAGGRIPLIIGRALTDRARNA 348

Query: 361 LGLPHSDVFR-QAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGP 419
           LG+  +DVF      V ++ +G+SLAQKMVG+ACGV+GI PG  CEPKMT+VGSQDTTGP
Sbjct: 349 LGMGATDVFTLPVNPVPKAGQGYSLAQKMVGKACGVEGILPGTACEPKMTTVGSQDTTGP 408

Query: 420 MTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVI 479
           MT DELK+LACL F + + MQSFCHTAAYPKP DV  H TLP FI  R GV L+PGDGVI
Sbjct: 409 MTADELKELACLKFLSPMFMQSFCHTAAYPKPADVKMHKTLPKFITERSGVPLKPGDGVI 468

Query: 480 HSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGK 539
           HSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFA A G MPLDMPESVLVRFKG+
Sbjct: 469 HSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAGALGFMPLDMPESVLVRFKGQ 528

Query: 540 MQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDAS 599
           + PGITLRD+V+AIP +AIKQG LTV KK K NIF+GRILE+EGLP+L VEQAFELTDA+
Sbjct: 529 LNPGITLRDVVNAIPYWAIKQGHLTVPKKNKVNIFNGRILEMEGLPELSVEQAFELTDAA 588

Query: 600 AERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQLLE 659
           AERSAA   IKL+++ +  YL SN+ L+K MIAEGY D +TL+ RI  + +WL  P+LLE
Sbjct: 589 AERSAAAGCIKLSEQSVATYLRSNVALMKKMIAEGYEDAKTLQNRIDAVNEWLKAPKLLE 648

Query: 660 ADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFRA 719
           ADA+AEYAAVI+I+LA+I EPIL  PNDPDD +LLS+V G  I +VF+GSCMTNIGHFRA
Sbjct: 649 ADANAEYAAVIEINLAEITEPILACPNDPDDVKLLSEVAGTPIQDVFLGSCMTNIGHFRA 708

Query: 720 AGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARV 779
           A ++    K     R W+ PPTRMD AQL +E  +S++   GARIEI GCSLCMGNQARV
Sbjct: 709 AAEIWRGQKFNPAVRTWICPPTRMDQAQLKDEALFSIYSAVGARIEIAGCSLCMGNQARV 768

Query: 780 ADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEY-QTYVAQVDKTAV 838
            DG  + STSTRNF +R+G GA V+L SAE+ AV + IGKLPTP EY   Y  +++    
Sbjct: 769 PDGVNMFSTSTRNFDDRIGNGAKVYLGSAEIGAVISNIGKLPTPAEYLAIYKEKIEPKKA 828

Query: 839 DTYRYLNFDQLSQY 852
           + Y+YL FD+++ Y
Sbjct: 829 EIYKYLQFDEMNGY 842


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: 1850
Number of extensions: 86
Number of successful extensions: 6
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: 843
Length adjustment: 42
Effective length of query: 823
Effective length of database: 801
Effective search space:   659223
Effective search space used:   659223
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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