Alignments for a candidate for acn in Novosphingobium fuchskuhlense FNE08-7

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Novosphingobium fuchskuhlense FNE08-7

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_067906659.1 AQZ52_RS04200 aconitate hydratase AcnA

Query= SwissProt::P37032
         (891 letters)



>NCBI__GCF_001519075.1:WP_067906659.1
          Length = 889

 Score = 1130 bits (2924), Expect = 0.0
 Identities = 575/893 (64%), Positives = 688/893 (77%), Gaps = 9/893 (1%)

Query: 2   KVGQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGN-TV 60
           +VGQD+L  +S LTV GK Y YY+L +A    +  ++RLP+S+KVLLENLLRFEDG  TV
Sbjct: 3   QVGQDTLGARSTLTVGGKDYAYYALGKAAAA-YGDVSRLPFSMKVLLENLLRFEDGGFTV 61

Query: 61  TTKDIKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKIS 120
           +T DIKA+ DW  + +S  EI +RP RVL+QDFTGVP VVDLAAMR AI K+GG+  +I+
Sbjct: 62  STDDIKALVDWQKDPSSSREIQYRPARVLLQDFTGVPCVVDLAAMRDAIAKLGGDTSRIN 121

Query: 121 PLSPVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTG 180
           PL PV LVIDHSVMVD+F    A E N +IE  RN ERY+FL+WG K+ +NF+ VPPGTG
Sbjct: 122 PLVPVHLVIDHSVMVDEFGHPKAFEQNVEIEYYRNGERYDFLKWGSKSLANFKAVPPGTG 181

Query: 181 ICHQVNLEYLGKTVWNSEN-DGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAM 239
           ICHQVNLE++ + VW SE  DG   AYPDT VGTDSHTTMINGLGVLGWGVGGIEAEAAM
Sbjct: 182 ICHQVNLEHIAQAVWTSEGPDGTTVAYPDTCVGTDSHTTMINGLGVLGWGVGGIEAEAAM 241

Query: 240 LGQPVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPL 299
           LGQPVSMLIPEV+GFK +G+LKEG+TATDLVLT T MLRK GVVG+FVE+YGPGL  L L
Sbjct: 242 LGQPVSMLIPEVVGFKFTGELKEGVTATDLVLTCTSMLRKHGVVGRFVEYYGPGLASLTL 301

Query: 300 ADRATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEE 359
           ADRAT++NMAPEYGATCGFF +D +T+ Y+ LTGRD++ IAL EAYAKAQG W D  + E
Sbjct: 302 ADRATLANMAPEYGATCGFFGIDDKTLDYMRLTGRDENQIALTEAYAKAQGFWIDP-SIE 360

Query: 360 PVFTDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKD 419
           PVFT +L LDLG+V PSLAGPKRPQD+V+L  +   FN  +    K+ ++     V+  D
Sbjct: 361 PVFTSTLELDLGTVVPSLAGPKRPQDRVSLPDVDDVFNADMANTYKKAQQR--VPVEGMD 418

Query: 420 FQMKHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDY 479
           F +  G V IAAITSCTNTSNP VL+AAGLVAKKA E GL+ KPWVK+SLAPGS+VVTDY
Sbjct: 419 FDIGDGDVTIAAITSCTNTSNPGVLVAAGLVAKKANELGLKPKPWVKTSLAPGSQVVTDY 478

Query: 480 LRHAGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGR 539
           L  AGLQ +LD +GFNLVGYGCTTCIGNSGPL + IS  + E+ LV ++V+SGNRNFEGR
Sbjct: 479 LVRAGLQEHLDAVGFNLVGYGCTTCIGNSGPLAEPISKAINENGLVAAAVISGNRNFEGR 538

Query: 540 VHPQVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEVA 599
           V P VRAN+LASPPLVVAYAL GT   D    PIGQ K+G DVYLKDIWPSN E+   +A
Sbjct: 539 VSPDVRANFLASPPLVVAYALKGTVIEDFVSTPIGQSKDGVDVYLKDIWPSNHEVYETMA 598

Query: 600 K-VSGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKP 658
             +   MF+  YA+V+KGDAHWQAI  +  +TY W   STY+ +PP+FE +++ P P+  
Sbjct: 599 GCMDRAMFQARYADVYKGDAHWQAINVAGSETYSWRAGSTYVANPPYFEGMTMTPAPVGD 658

Query: 659 IKQAYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMR 718
           I +A  LA+ GDSITTDHISPAGSIKA SPAG +L    V + DFNSYG+RRG+HEVMMR
Sbjct: 659 IIEAKPLAILGDSITTDHISPAGSIKADSPAGKWLMEHQVAKADFNSYGARRGHHEVMMR 718

Query: 719 GTFANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSR 778
           GTFANIRI+NEM PG EGG++RY    E  +IYD AM+++ +   LV+IAGKEYGTGSSR
Sbjct: 719 GTFANIRIKNEMVPGIEGGMSRY--GAEVGAIYDVAMQHKADGTPLVVIAGKEYGTGSSR 776

Query: 779 DWAAKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIEIS 838
           DWAAKGTNLLGV+AVI ESFERIHRSNL+GMG+LPLQFK+G +R+TL L G +  +I   
Sbjct: 777 DWAAKGTNLLGVRAVIVESFERIHRSNLVGMGVLPLQFKDGESRQTLGLTGDDTFTIRGV 836

Query: 839 DKLTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKISS 891
             L P   V V + R DG       LCRIDTA+ELEYY NGGIL YVLR +++
Sbjct: 837 AGLKPRQDVEVEVTRADGSTFTFTALCRIDTANELEYYLNGGILHYVLRNLAA 889


Lambda     K      H
   0.316    0.134    0.393 

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: 2184
Number of extensions: 112
Number of successful extensions: 8
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: 891
Length of database: 889
Length adjustment: 43
Effective length of query: 848
Effective length of database: 846
Effective search space:   717408
Effective search space used:   717408
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.

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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