Alignments for a candidate for acn in Lacinutrix algicola AKS293

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Lacinutrix algicola AKS293

Align Aconitate hydratase B; ACN; Aconitase; EC 4.2.1.3; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; EC 4.2.1.99; Iron-responsive protein-like; IRP-like; RNA-binding protein (uncharacterized)
to candidate WP_055435324.1 ASC41_RS03870 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= curated2:Q9ZL64
         (852 letters)



>NCBI__GCF_001418085.1:WP_055435324.1
          Length = 924

 Score =  299 bits (766), Expect = 4e-85
 Identities = 275/917 (29%), Positives = 433/917 (47%), Gaps = 119/917 (12%)

Query: 7   DYKKSVLERKSEGIPPLPLNAKQVEAVVEILMKDPTNAAFAKEL--LIHRVSPGVDEGAK 64
           DY K +  RK +G+ P P++  ++ + +   +KD  N    + L   I+ V PG    A 
Sbjct: 6   DYLKQIENRKEQGLHPQPIDGAELLSQIIEQIKDLDNEHREESLNFFIYNVLPGTTSAAT 65

Query: 65  VKAEFLAQLSQKKLECPHISALEATTLLGTMLGGYNVEPLIVGLESQDKNIAKESAKALK 124
           VKA+FL ++   +     I+   A   L  M GG +V+ L+      D ++AK+SA+ LK
Sbjct: 66  VKAKFLKEIILGESIVKEITPTFALEQLSHMKGGPSVKVLLDIALGNDADLAKQSAEILK 125

Query: 125 TTLLVY-GSFDKIAAMSKTNA-LAKEVLESWANAEWFLNKEPLNECIEACVFKID-GETN 181
           T + +Y    D++    K+ + +AK+++ES+A AE+F     ++E IE   +    G+ +
Sbjct: 126 TQVFLYEADTDRLEEAFKSGSEIAKDIIESYAKAEFFTKLPEIDEKIEVVTYIAGVGDIS 185

Query: 182 TDDLSPASDAFTRSDIPLHAKAMLKNRIENYEQRIEAIKT----KGVPVAYVGDVVGTGS 237
           TD LSP  DA +RSD  LH + M ++  ++ +  + A+K     K V +      +G GS
Sbjct: 186 TDLLSPGGDAHSRSDRELHGQCMFEHN-KDMQNELLALKEQHPDKRVMLIAEKGTMGVGS 244

Query: 238 SRKSATNSI-MWH---FGKDIPFVPNKRSGGIVIGGV--IAPIFFATCEDSGAL------ 285
           SR S  N++ +W    F K +PF+    +   VI G   IAPIF  T   +G +      
Sbjct: 245 SRMSGVNNVALWTGVPFSKYVPFI----NFAPVIAGTNGIAPIFLTTVGVTGGIGLDLKN 300

Query: 286 ------------------PIVADVKDLKEGDIIKIYPYKGEITLNDKVVSTFK--LEPET 325
                             PI+ +   +  G I+ I   + ++   DK +        P+ 
Sbjct: 301 WVQQKDAEGNTVRDEDGEPILKETYSVATGTILTINTKEKKLYNGDKELKDISAAFTPQK 360

Query: 326 LLDEVRASGRIPLIIGRGLTNKARKFLGLGESEAFKKPSAPKSDAKGYTLAQKIVG-HAC 384
           + + ++A G   ++ G+ L   A K LG+   + +        + +G T  +KI   +A 
Sbjct: 361 M-EFMKAGGSYAVVFGKKLQTFAAKALGIEAPQVYATAKEVSIEGQGLTAVEKIFNKNAV 419

Query: 385 GVKG--ILPGAYCEPKVTTVGSQDTTGAMTRDEVKELASLKFDAPFV---LQSFCHTAAY 439
           G  G  +  G+Y   +V  VGSQDTTG MT  E++ +A+    +P V    QS CHTA+ 
Sbjct: 420 GTSGATLHAGSYVRAEVNIVGSQDTTGLMTSQELEMMAATVI-SPIVDGAYQSGCHTASV 478

Query: 440 PKPSDVSLHATLP---------GFITQRGGVALH-PGDGVIHTWLNRMGLPD-TLGTGGD 488
               D    A +P         G IT R     + P   VIH  LN + + D  +  GGD
Sbjct: 479 ---WDDKSKANIPRLMSFMNDFGLITGRDPKGKYFPMTDVIHKVLNDITVGDWDIIIGGD 535

Query: 489 SHTRFPLGISFPAGSGLVAFAAVTGTMPLNMPESVLVRFKGEMNPGITLRDLVNAIPYYA 548
           SHTR   G++F A SG VA A  TG   + +PESV V FKG+M   +  RD+V+A     
Sbjct: 536 SHTRMSKGVAFGADSGTVALALATGEASMPIPESVKVTFKGQMKSYMDFRDVVHATQQQM 595

Query: 549 IKKGLLTVEKKGKINVFNGRILEIEGLPDIKMEQAFELSDASAERSAAACVVRLNKEPMI 608
           +K       + G  NVF GR++E+  +  +  ++AF  +D +AE  A A +     + +I
Sbjct: 596 LK-------QFGGENVFQGRVIEVH-IGTLTADEAFTFTDWTAEMKAKASICISEDDTLI 647

Query: 609 EYLKSNIKLIDEMIASGYED-KETLKKRRDAMQAWV------DKPVLLEPDSNAQYAAVI 661
           E L+     I  MI  G ++ K+ LK   D  +  +       KP  L PD+NA+Y A +
Sbjct: 648 ESLEIAKGRIQIMIEKGMDNAKQVLKGLVDKAETRIIELKTGMKP-SLRPDANAKYHAEV 706

Query: 662 EIDVAEITEPILACPN-DPDDVA---TLSEVLADTTGKRPHAIDEVFIGSCMTNIGHFRA 717
            ID+ +I EP++A P+ + +DV+   T   +   +       +D  F+GSCM + G  + 
Sbjct: 707 IIDLDQIVEPMIADPDVNNEDVSKRYTHDNIRPLSYYGGTKKVDLGFVGSCMVHKGDMKI 766

Query: 718 FGEIVKNAPPS------QARLWVVPPSKMDEQELINEGYYAIF------------GAAGA 759
             +++KN          +A L V PP+     EL  EG + +                 A
Sbjct: 767 LAQMLKNVEAQYGKVEFKAPLIVAPPTYNIVDELKAEGDWEVLVRYSGFEFDDNAPKGEA 826

Query: 760 RT--------EVPGCSLCMGNQARVRDNAVVFSTSTRNFDNRMGRGA-----KVYLGSAE 806
           RT        E PGC+LCMGNQ +      V +TSTR F  R+ + +     +  L S  
Sbjct: 827 RTGYENMLYLERPGCNLCMGNQEKAAPGDTVMATSTRLFQGRVVKDSGEKKGESLLSSTP 886

Query: 807 LGAACALLGRIPTKEEY 823
           +     +LGR PT EEY
Sbjct: 887 VVVLSTILGRTPTMEEY 903


Lambda     K      H
   0.317    0.135    0.390 

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: 1689
Number of extensions: 85
Number of successful extensions: 14
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: 852
Length of database: 924
Length adjustment: 43
Effective length of query: 809
Effective length of database: 881
Effective search space:   712729
Effective search space used:   712729
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 (21.6 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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