Alignments for a candidate for acn in Nitratifractor salsuginis DSM 16511

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Nitratifractor salsuginis DSM 16511

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_013553742.1 NITSA_RS04000 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>NCBI__GCF_000186245.1:WP_013553742.1
          Length = 857

 Score = 1097 bits (2836), Expect = 0.0
 Identities = 553/860 (64%), Positives = 674/860 (78%), Gaps = 22/860 (2%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           ++E+Y+KH  ERA  G+ P PL A Q A LVELLK  P+ EEE+LLDLL N V PGVD+A
Sbjct: 3   LIEDYKKHTEERAKLGVPPLPLTAQQTAELVELLKQDPIPEEEYLLDLLKNHVNPGVDDA 62

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDAL--DDAKLAPIAAKA 118
           AYVKA FL  + +G   S  +SP +A+ +LG M GGYN+ PL+DAL   DA++A  AA  
Sbjct: 63  AYVKAAFLNDIVQGKAQSKAISPVEAVRILGMMLGGYNVGPLVDALKHSDAEIAQAAADE 122

Query: 119 LSHTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETN 178
           L HT+L++D F DV+E    GNEYAKQV++SWA+AEWFL+R PL E++ +TVFKV GETN
Sbjct: 123 LKHTILVYDAFNDVKELMDQGNEYAKQVIESWANAEWFLNREPLPEEMKLTVFKVPGETN 182

Query: 179 TDDLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGD 238
           TDDLSPA +A++R DIPLHAQ+ML N  +           P++ I+ L+++G  LAYVGD
Sbjct: 183 TDDLSPASEAFTRSDIPLHAQSMLVNRMDN----------PLETIKKLKERGNDLAYVGD 232

Query: 239 VVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298
           VVGTGSSRKS  NSV W+ G DIP VPNKR GG+ +G  IAPIFFNT ED+G LPIE  V
Sbjct: 233 VVGTGSSRKSGINSVQWWFGHDIPGVPNKRTGGVVIGSIIAPIFFNTAEDSGCLPIEAPV 292

Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
             L  GD I V PY+G++  +  GE+++ F LK + L DE+RAGGRIPLIIG+GLT KAR
Sbjct: 293 DALETGDEIVVKPYEGKILKN--GEVVSEFTLKPNTLPDEMRAGGRIPLIIGKGLTNKAR 350

Query: 359 EALGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTG 418
           EALGL HSDVF + +  A+S +G++LAQKMVG+ACG++G+RPG Y EP +T+VGSQDTTG
Sbjct: 351 EALGLGHSDVFTKPEQPADSGKGYTLAQKMVGKACGMEGVRPGMYVEPVVTTVGSQDTTG 410

Query: 419 PMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGV 478
           PMTRDE+K+LA L F ADLV+Q+FCHTAAYPKP DV   HTLP F  +RGGV L+PGDGV
Sbjct: 411 PMTRDEIKELAALSFGADLVLQTFCHTAAYPKPADVELQHTLPPFWTSRGGVILKPGDGV 470

Query: 479 IHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKG 538
           IHSWLNRM+LPDTVGTGGDSHTRFPIGISFPAGSGLVAFAA TG+MPL+MPESVLV+FKG
Sbjct: 471 IHSWLNRMILPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAVTGMMPLNMPESVLVKFKG 530

Query: 539 KMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDA 598
           +MQPGITLRDLV+AIP  AIK+GLLTVEKKGKKN+F+GRILEIEGL DLKVEQAFEL+DA
Sbjct: 531 EMQPGITLRDLVNAIPYQAIKEGLLTVEKKGKKNVFAGRILEIEGLEDLKVEQAFELSDA 590

Query: 599 SAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQLL 658
           SAERSAA CT+KLNKEP++EYL SNI LL+ MI +GY D+RTL+RRI  M+ WL +P L+
Sbjct: 591 SAERSAAACTVKLNKEPVIEYLRSNIKLLEKMIEQGYEDKRTLQRRIDKMKAWLENPTLM 650

Query: 659 EADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEK-----IDEVFIGSCMTN 713
           E D DAEYAAVI+IDL +I EPI+  PNDPDD   LS+V  ++     IDEVF+GSCMTN
Sbjct: 651 ERDEDAEYAAVIEIDLNEITEPIVACPNDPDDVATLSEVLADEKRPKNIDEVFVGSCMTN 710

Query: 714 IGHFRAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCM 773
           IG FRA G++L   +G + TRLWV PPT+MD  +L EEGYY++FG++GAR EIPGCSLCM
Sbjct: 711 IGLFRALGEVLKG-EGPVDTRLWVTPPTKMDQKELIEEGYYAIFGQAGARTEIPGCSLCM 769

Query: 774 GNQARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQ- 832
           GNQARV D + V STSTRNF NR+G GA V+L S+ELAAV AL+G++P+ EEY   V + 
Sbjct: 770 GNQARVRDNSVVFSTSTRNFDNRMGKGAQVYLGSSELAAVCALLGRIPSKEEYLEIVNKK 829

Query: 833 -VDKTAVDTYRYLNFDQLSQ 851
             D      Y+YLNFDQ+ +
Sbjct: 830 ITDDKKDQVYKYLNFDQIPE 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: 2001
Number of extensions: 81
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: 857
Length adjustment: 42
Effective length of query: 823
Effective length of database: 815
Effective search space:   670745
Effective search space used:   670745
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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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 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