Alignments for a candidate for acn in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Stenotrophomonas chelatiphaga DSM 21508

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_057687520.1 ABB28_RS16835 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>NCBI__GCF_001431535.1:WP_057687520.1
          Length = 863

 Score = 1261 bits (3264), Expect = 0.0
 Identities = 625/859 (72%), Positives = 728/859 (84%), Gaps = 8/859 (0%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           MLE YR HVAERAA GI P PL A Q A ++ELLK PP GE EFLLDLL +RVP GVD+A
Sbjct: 1   MLEAYRHHVAERAALGIPPLPLTAQQTADVIELLKNPPAGEAEFLLDLLTHRVPAGVDDA 60

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A VKA +LAA+A G   +PL+S E+A ELLGTM GGYN+ PL+  LDDA +  IAA AL 
Sbjct: 61  AKVKASYLAAIAFGSEQNPLISRERATELLGTMLGGYNVAPLVQLLDDATVGSIAAAALK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
           +TLL+FD F+DV+EKAKAGN  A+ V+QSWADAEWF SRP +A+ +T+TVFKV GETNTD
Sbjct: 121 NTLLVFDAFHDVQEKAKAGNANAQSVLQSWADAEWFTSRPEVAQSMTLTVFKVPGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNARE--GIEPDQPGVVGPIKQIEALQKKGYPLAYVGD 238
           DLSPAPDA +RPDIPLHA AMLKN R      P++ G  GPI++I +L+ KG+ +AYVGD
Sbjct: 181 DLSPAPDATTRPDIPLHALAMLKNKRPDAAFVPEEDGKRGPIQEILSLKDKGHLVAYVGD 240

Query: 239 VVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298
           VVGTGSSRKSATNSVLWF G+DIP +PNKR GG+CLG KIAPIF+NTMEDAGALPIE+DV
Sbjct: 241 VVGTGSSRKSATNSVLWFTGEDIPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDV 300

Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
           + +  GDVI++ PY G+   +  GE++A F++K+DVL DEVRAGGRIPLI+GRGLT KAR
Sbjct: 301 TQMEHGDVIELRPYDGKALKN--GEVIAEFQVKSDVLFDEVRAGGRIPLIVGRGLTAKAR 358

Query: 359 EALGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415
           EALG+P +D+FR     A++ +GFSLAQKMVGRACG+   +G+RPG YCEPKMTSVGSQD
Sbjct: 359 EALGMPVTDLFRLPVQPADTGKGFSLAQKMVGRACGLPEGQGMRPGTYCEPKMTSVGSQD 418

Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPG 475
           TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THHTLP+FI  RGG+SLRPG
Sbjct: 419 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHTLPEFISTRGGISLRPG 478

Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535
           DGVIHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVR
Sbjct: 479 DGVIHSWLNRMLLPDTVGTGGDSHTRFPVGISFPAGSGLVAFAAATGVMPLDMPESVLVR 538

Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595
           FKGKMQPG+TLRDLV+AIPLYAIK GLLTV K GKKNIFSGRILEIEGLPDLKVEQAFEL
Sbjct: 539 FKGKMQPGVTLRDLVNAIPLYAIKAGLLTVAKAGKKNIFSGRILEIEGLPDLKVEQAFEL 598

Query: 596 TDASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADP 655
           +DASAERSAAGC++ L+K PI+EYLTSNI LL+WMIAEGY D R+L+RRI  M++WLADP
Sbjct: 599 SDASAERSAAGCSVHLDKAPIIEYLTSNITLLQWMIAEGYQDPRSLQRRIDKMKEWLADP 658

Query: 656 QLLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIG 715
           QLL  DADAEYAAVI+IDLADI EPI+  PNDPDD ++LS+V G KIDEVFIGSCMTNIG
Sbjct: 659 QLLAPDADAEYAAVIEIDLADIHEPIVACPNDPDDVKMLSEVAGAKIDEVFIGSCMTNIG 718

Query: 716 HFRAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775
           HFRAA KLL+  K  +PT+LWVAPPT+MDA++LT EG+Y  FG +GAR+E+PGCSLCMGN
Sbjct: 719 HFRAAAKLLEG-KRDIPTKLWVAPPTKMDASELTREGHYGTFGSAGARMEMPGCSLCMGN 777

Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835
           QA+V +GATV STSTRNFPNRLG  +NV+L SAELAA+ + +G++PT EEY   V  ++ 
Sbjct: 778 QAQVREGATVFSTSTRNFPNRLGRNSNVYLGSAELAAICSRLGRIPTKEEYMADVGVLEA 837

Query: 836 TAVDTYRYLNFDQLSQYTE 854
           +  + YRY+NFDQ+ +Y E
Sbjct: 838 SGAEIYRYMNFDQIEEYQE 856


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: 2096
Number of extensions: 78
Number of successful extensions: 5
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: 863
Length adjustment: 42
Effective length of query: 823
Effective length of database: 821
Effective search space:   675683
Effective search space used:   675683
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