Alignments for a candidate for acn in Geobacter metallireducens GS-15

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Geobacter metallireducens GS-15

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_011365887.1 GMET_RS09660 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_000012925.1:WP_011365887.1
          Length = 847

 Score = 1025 bits (2649), Expect = 0.0
 Identities = 535/858 (62%), Positives = 640/858 (74%), Gaps = 18/858 (2%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           M+E Y  H AER A+GI   PL+  Q A L  LL+NPPAG+EEFLL+LL  RV PGVD A
Sbjct: 1   MIEAYLAHEAERKAQGIPALPLNPEQTADLCNLLQNPPAGKEEFLLNLLKERVSPGVDPA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A VKA FLA I KG  KSPL++   AI +LGTM GGYN+ PL++AL DA+LA  AA ALS
Sbjct: 61  AKVKAAFLAEIVKGTKKSPLVSKVDAIRILGTMIGGYNVGPLVEALKDAELAEEAACALS 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
              L++D F  V E +K+ N  AK+V++SWA+AEWF NRP + E + V VFKV GE NTD
Sbjct: 121 RMTLVYDGFDQVVELSKS-NAAAKKVLESWANAEWFTNRPGVPETIKVKVFKVEGEINTD 179

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           D SPA DAWSRPDIPLHALAM K       P++      +K I   +  G  +A+VGDVV
Sbjct: 180 DFSPAGDAWSRPDIPLHALAMGKTRF----PNR------LKDIADWRAAGHQVAFVGDVV 229

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSA NSVLW MG DIP VPNK+  G+ +GG IAPIFFNT +D+GALP++ DV+ 
Sbjct: 230 GTGSSRKSACNSVLWHMGQDIPAVPNKKTAGVIIGGVIAPIFFNTAQDSGALPLKADVTK 289

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           +N GDVI +   KGE+ N + GE+++TF++  + L DE RAGGRIPLIIGR +T KAR+A
Sbjct: 290 MNDGDVITINTAKGEISN-DKGEVISTFKISPNTLADEFRAGGRIPLIIGRAITEKARKA 348

Query: 361 LGLPHSDVFRQAKDVA-ESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGP 419
           LGL  +DVF +  + A ++ +G+SLAQKMVG+ACGV GI PG  CEPKMT+VGSQDTTGP
Sbjct: 349 LGLGDTDVFTKPVNPAPKAGQGYSLAQKMVGKACGVAGILPGTACEPKMTTVGSQDTTGP 408

Query: 420 MTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVI 479
           MT DELK+LACL F + + MQSFCHTAAYPKP DV  H  LP FI+ RGGV L+PGDGVI
Sbjct: 409 MTADELKELACLKFLSPMFMQSFCHTAAYPKPADVKMHKNLPGFIIERGGVPLKPGDGVI 468

Query: 480 HSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGK 539
           HSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFA A G MPLDMPESVLVRFKGK
Sbjct: 469 HSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAGAMGFMPLDMPESVLVRFKGK 528

Query: 540 MQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDAS 599
           + PGITLRD V+AIP +AIKQG LTV KK K NIF+GRILE+EGLPDL VEQAFELTDA+
Sbjct: 529 LNPGITLRDAVNAIPYWAIKQGKLTVPKKNKINIFNGRILEMEGLPDLTVEQAFELTDAA 588

Query: 600 AERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLE 659
           AERSAA   I+L+KE +  YL SN+ L+K MIA+GY D +TL+ RI  + +WL NP+LLE
Sbjct: 589 AERSAAAGCIQLSKESVATYLRSNVALMKKMIADGYQDAQTLQNRIDAVNEWLKNPQLLE 648

Query: 660 ADADA----EYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIG 715
           AD +A     YA VI+IDLA+I EPIL  PNDPDD + LS V G  I +VF+GSCMTNIG
Sbjct: 649 ADKNAVETGAYADVIEIDLAEITEPILACPNDPDDVKLLSDVAGTPIQDVFLGSCMTNIG 708

Query: 716 HFRAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775
           HFRAA ++    K     R W+ PPTRMD  QL +E Y+SV+   GARIEI GCSLCMGN
Sbjct: 709 HFRAAAEIWRGLKFNPSVRTWICPPTRMDQKQLKDEAYFSVYSAFGARIEIAGCSLCMGN 768

Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQ-TYVAQVD 834
           QARV DG  + STSTRNF +R+G GA VFL SAEL AV A +GKLPT  E+   Y  +V+
Sbjct: 769 QARVPDGVNMFSTSTRNFDDRIGDGAKVFLGSAELGAVTATLGKLPTVAEFMAAYKEKVE 828

Query: 835 KTAVDTYRYLNFNQLSQY 852
                 Y+YL F+++ +Y
Sbjct: 829 PKKDVVYKYLQFDEMPEY 846


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: 1903
Number of extensions: 80
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: 847
Length adjustment: 42
Effective length of query: 823
Effective length of database: 805
Effective search space:   662515
Effective search space used:   662515
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