Alignments for a candidate for acn in Methylococcus capsulatus str. Bath

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Methylococcus capsulatus str. Bath

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_010961708.1 MCA_RS12190 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_000008325.1:WP_010961708.1
          Length = 858

 Score = 1319 bits (3413), Expect = 0.0
 Identities = 643/856 (75%), Positives = 742/856 (86%), Gaps = 7/856 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           ML +YR+HVAERAA+G+ PKPL A Q AALVELLK+PPAGEE FLLDLL+NRVP GVDEA
Sbjct: 1   MLTQYREHVAERAAQGLVPKPLTAEQTAALVELLKSPPAGEEAFLLDLLSNRVPAGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFLAA+A+GEA SP+++P +A ELLGTM GGYN+ PLI+ LD ++LAP+AA  LS
Sbjct: 61  AYVKAGFLAAVARGEAVSPIVSPRRATELLGTMLGGYNVAPLIELLDHSELAPVAAHGLS 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
            TLLMFD F+DV+ KA+AGN +A+ V+++WADAEWF +RP +  KLTVTVFKV GETNTD
Sbjct: 121 RTLLMFDAFHDVQVKAEAGNVHAQAVLRAWADAEWFTSRPEVPGKLTVTVFKVPGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPA DAWSRPDIPLHA +MLK  REGI   +        QI  L+ KGFP+AYVGDVV
Sbjct: 181 DLSPAQDAWSRPDIPLHAKSMLKVPREGIHDAEA-------QIAELKTKGFPVAYVGDVV 233

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNS+LW++G+DIPHVPNKR GG+C+GGKIAPIFFNT+ED+GALPIE DV+ 
Sbjct: 234 GTGSSRKSATNSLLWYIGEDIPHVPNKRQGGVCIGGKIAPIFFNTLEDSGALPIECDVTA 293

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           +  GDVID++PY+G +RNHE+G  L  F LKT++L+DEVRAGGRI LIIGRGLT +AR+ 
Sbjct: 294 MQTGDVIDIHPYEGVLRNHESGVELCRFTLKTEILLDEVRAGGRINLIIGRGLTDRARKV 353

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGLP S+VFR+ +   E+ +G++LAQK+VG+ACGV GIRPG YCEP MT+VGSQDTTGPM
Sbjct: 354 LGLPPSEVFRRPRAPIETGKGYTLAQKIVGKACGVAGIRPGTYCEPAMTTVGSQDTTGPM 413

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFSADLV+QSFCHTAAYPKPVDV THHTLPDFIMNRGGVSLRPGDG+IH
Sbjct: 414 TRDELKDLACLGFSADLVLQSFCHTAAYPKPVDVETHHTLPDFIMNRGGVSLRPGDGIIH 473

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKG+M
Sbjct: 474 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGEM 533

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPGITLRDLVHAIP  A+++GLLTVEK+GKKN+FSGRILEIEGLPDLKVEQAFEL DASA
Sbjct: 534 QPGITLRDLVHAIPYVALQRGLLTVEKQGKKNVFSGRILEIEGLPDLKVEQAFELADASA 593

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAA CTIKL++ PI EYL+SNI LL+WMIAEGYGD RTL RRI  ME WLA+P+LLEA
Sbjct: 594 ERSAAACTIKLDRAPIEEYLHSNITLLRWMIAEGYGDARTLRRRIAAMEAWLADPQLLEA 653

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           D DAEYA VI+IDL  I EP+LC PNDPDD +PLS V G  IDEVF+GSCMTNIGHFRAA
Sbjct: 654 DPDAEYAEVIEIDLDQITEPLLCCPNDPDDVKPLSQVAGTHIDEVFLGSCMTNIGHFRAA 713

Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           G+LL+A     PTRLW+APPTRMD AQLTEEGYY+ +GK+GAR E+PGCSLCMGNQARVA
Sbjct: 714 GRLLEAFGKPTPTRLWIAPPTRMDQAQLTEEGYYATYGKAGARTEMPGCSLCMGNQARVA 773

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
           D ATVVSTSTRNFPNRLG GA VFLASAELAAV +++G++P+ EEY  Y  ++++ A DT
Sbjct: 774 DNATVVSTSTRNFPNRLGAGARVFLASAELAAVCSILGRIPSLEEYMAYAGKIEEKAADT 833

Query: 841 YRYLNFNQLSQYTEKA 856
           YRYLNF++   Y E+A
Sbjct: 834 YRYLNFDRTPAYAERA 849


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: 2025
Number of extensions: 69
Number of successful extensions: 2
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: 858
Length adjustment: 42
Effective length of query: 823
Effective length of database: 816
Effective search space:   671568
Effective search space used:   671568
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