Alignments for a candidate for acn in Oleispira antarctica RB-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Oleispira antarctica RB-8

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_046008325.1 OLEAN_RS05010 aconitate hydratase AcnA

Query= SwissProt::P37032
         (891 letters)



>NCBI__GCF_000967895.1:WP_046008325.1
          Length = 897

 Score = 1106 bits (2861), Expect = 0.0
 Identities = 563/890 (63%), Positives = 674/890 (75%), Gaps = 4/890 (0%)

Query: 1   MKVGQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTV 60
           MK   ++ +T S LTV+ K + Y+++   E    K I RLP ++K+LLEN+LR EDG + 
Sbjct: 1   MKNSDNTFNTLSTLTVNDKPFRYFAINGGELASHKTIARLPLTIKILLENMLRNEDGLSC 60

Query: 61  TTKDIKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKIS 120
              DI+A+A     K S+ EIA+ P RVLMQDFTGVPAVVDLAAMR A+VK G +   I+
Sbjct: 61  RRDDIEALAA-SGGKASEQEIAYHPARVLMQDFTGVPAVVDLAAMRDALVKRGIDPQTIN 119

Query: 121 PLSPVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTG 180
           PL+ VDLVIDHS+ +DKFAS  A E N  IE++RN ERY+FL+WGQ AF+NF VVPPGTG
Sbjct: 120 PLTKVDLVIDHSISIDKFASESAFEENVAIEMQRNHERYQFLKWGQSAFANFSVVPPGTG 179

Query: 181 ICHQVNLEYLGKTVWNSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAML 240
           ICHQVNLEYL K VW  + DG+ +AYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAA+L
Sbjct: 180 ICHQVNLEYLAKVVWTEDKDGERFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAIL 239

Query: 241 GQPVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLA 300
           GQP+SMLIP+V+G +L+GKL EGITATDLVLTV +MLR+ GVVGKFVEFYG GL+ LPLA
Sbjct: 240 GQPISMLIPDVVGVELTGKLLEGITATDLVLTVVEMLREYGVVGKFVEFYGAGLDHLPLA 299

Query: 301 DRATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEP 360
           DRATI+NMAPEYGATCGFFPVDK+TI YL L+GRD+  I LVEAY KAQG+W D+    P
Sbjct: 300 DRATIANMAPEYGATCGFFPVDKQTINYLRLSGRDEEQIELVEAYCKAQGLWRDEHFLVP 359

Query: 361 VFTDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDF 420
            F+ +L LDL ++ PSLAGPKRPQD+V ++ L       +   GK K+    + +   + 
Sbjct: 360 DFSATLRLDLTTIVPSLAGPKRPQDRVPVTGLKTAVAGSIELAGKAKQLNTEYPLAGSEV 419

Query: 421 QMKHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYL 480
            M HG VVIAAITSCTNTSNP+V++AAGLVA+ A+ KGLQRK WVKSSLAPGSKVVT+YL
Sbjct: 420 AMHHGDVVIAAITSCTNTSNPAVMIAAGLVARNALAKGLQRKSWVKSSLAPGSKVVTEYL 479

Query: 481 RHAGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRV 540
           + A LQ  LD+LGFNLVGYGCTTCIGNSGPLP+ +   +A +DL+VSSVLSGNRNFEGR+
Sbjct: 480 QQAKLQEPLDKLGFNLVGYGCTTCIGNSGPLPEVVEATIAANDLIVSSVLSGNRNFEGRI 539

Query: 541 HPQVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEVAK 600
           HP V+ NWLASPPLVVAYAL GTT  DLSR+ +G D  G  VYLKDIWP+N EIA  V  
Sbjct: 540 HPLVQDNWLASPPLVVAYALAGTTRIDLSRDSLGNDDNGQPVYLKDIWPTNVEIAELVQA 599

Query: 601 VSGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIK 660
           ++ TMF KEY+ VF GD  W+AI + +G+TY++  DSTYIQ PPFFE           I 
Sbjct: 600 ITSTMFNKEYSAVFDGDDRWRAIDSGNGKTYKFTEDSTYIQLPPFFEERYRGKS--SSII 657

Query: 661 QAYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGT 720
           +A +LA+ GDS+TTDHISPAG+I   SPA  YL+++G+ EKDFNSYGSRRGNH+VM+RGT
Sbjct: 658 KAPMLAMLGDSVTTDHISPAGAIPQDSPASQYLRAQGIAEKDFNSYGSRRGNHKVMVRGT 717

Query: 721 FANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDW 780
           F NIRIRNEMTP  EGG TR     +   IYDAAM YQ    D V++AGKEYGTGSSRDW
Sbjct: 718 FGNIRIRNEMTPELEGGYTRMQGEHQPRFIYDAAMLYQSKNIDTVVVAGKEYGTGSSRDW 777

Query: 781 AAKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISI-EISD 839
           AAKGT LLGVKAVI ESFERIHRSNL+GMG+LPLQF  G TRKTL L G E   I  + +
Sbjct: 778 AAKGTLLLGVKAVIVESFERIHRSNLVGMGVLPLQFMPGETRKTLSLTGEETFDIVGLDE 837

Query: 840 KLTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKI 889
            L P   V  TI    G++  I+   R+DTA E++YY  GG+L YVL +I
Sbjct: 838 PLLPKQEVVATIYYPSGEVRPIKLQSRLDTAVEVKYYLAGGVLSYVLDQI 887


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: 2043
Number of extensions: 84
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: 891
Length of database: 897
Length adjustment: 43
Effective length of query: 848
Effective length of database: 854
Effective search space:   724192
Effective search space used:   724192
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 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