Alignments for a candidate for acn in Psychromonas ingrahamii 37

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Psychromonas ingrahamii 37

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_011770425.1 PING_RS10955 aconitate hydratase AcnA

Query= SwissProt::P37032
         (891 letters)



>NCBI__GCF_000015285.1:WP_011770425.1
          Length = 891

 Score = 1091 bits (2822), Expect = 0.0
 Identities = 543/886 (61%), Positives = 667/886 (75%), Gaps = 4/886 (0%)

Query: 7   SLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTKDIK 66
           ++  K+  TV+G+ Y+YY++ + E      I RLP S+KVLLENLLR +  N  + K+I+
Sbjct: 7   NIDAKNTFTVNGQVYSYYAINKGELAGNDSITRLPVSIKVLLENLLRHQQDNGGSRKEIE 66

Query: 67  AIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLSPVD 126
           A+A     + S  EI ++P RVLMQDFTGVPAVVDLAAMR A+VK G +  KI+PL+ VD
Sbjct: 67  ALAS-SQGRGSTTEINYQPARVLMQDFTGVPAVVDLAAMRNALVKQGLDPQKINPLAKVD 125

Query: 127 LVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICHQVN 186
           LVIDHSV VDKF+S  A + N  IE+ RNKERYEFL+WG++AF NF VVPPGTGICHQVN
Sbjct: 126 LVIDHSVNVDKFSSKSAFDENVAIEMARNKERYEFLKWGKQAFENFSVVPPGTGICHQVN 185

Query: 187 LEYLGKTVWNSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSM 246
           LEYL K VW+   + +   YPDTLVGTDSHTTMIN LGVLGWGVGGIEAEA MLGQP+SM
Sbjct: 186 LEYLAKVVWSETTENESLVYPDTLVGTDSHTTMINALGVLGWGVGGIEAEAVMLGQPISM 245

Query: 247 LIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADRATIS 306
            IP+V+GF+L+G+L EGITATDLVL V QMLRK GVVGKFVEFYG GL  LPLADRATI+
Sbjct: 246 QIPDVVGFELTGRLAEGITATDLVLQVVQMLRKHGVVGKFVEFYGAGLAHLPLADRATIA 305

Query: 307 NMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVFTDSL 366
           NMAPEYGATCGFFPVD++T+ YL+LTGRDK TI LVE+Y+K QG+W D+   +  F+D+L
Sbjct: 306 NMAPEYGATCGFFPVDQQTLNYLQLTGRDKQTIDLVESYSKLQGLWRDETTPKADFSDTL 365

Query: 367 HLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDFQMKHGH 426
            LD+  +EP+LAGP RPQD+V +  L    ++F+   GK ++K   F + + D  + HG 
Sbjct: 366 LLDMSDIEPNLAGPDRPQDRVPMRQLKTATDDFIDLNGKGQQKTTDFPINDSDQSLHHGS 425

Query: 427 VVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRHAGLQ 486
           +VIAAITSCTNTSNP+V++AAGL+AKKA+ KGL ++PWVK+SLAPGS+VVTDYL   GLQ
Sbjct: 426 LVIAAITSCTNTSNPAVMLAAGLLAKKALAKGLVKQPWVKTSLAPGSRVVTDYLVETGLQ 485

Query: 487 TYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHPQVRA 546
             L+ LGFNLVGYGCTTCIGNSGPLP  +  C+ E+DL+VS+VLSGNRNF GR+HPQV+A
Sbjct: 486 QSLNTLGFNLVGYGCTTCIGNSGPLPKPVQECIEENDLIVSAVLSGNRNFAGRIHPQVKA 545

Query: 547 NWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEVAKVSGTMF 606
           +WLASPPLVVAY+L GTT  DLS++PIG   +G  VYLKDIWPSN EI   +  VS  MF
Sbjct: 546 SWLASPPLVVAYSLAGTTRIDLSQDPIGTGSDGEKVYLKDIWPSNAEITELLKSVSHQMF 605

Query: 607 RKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQAYVLA 666
            K Y+ VF GD  WQAIQ+     Y+++ +STYIQ PPFFE      +    I  A +L 
Sbjct: 606 EKRYSAVFDGDKEWQAIQSGEEANYQFSDESTYIQKPPFFE--PQYRDNFSNIVDAPILV 663

Query: 667 LFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTFANIRI 726
           + GDS+TTDHISPAG+I   SPA  +L++ G+DEKDFNSYGSRRGNHE+MMRGTF NIRI
Sbjct: 664 MLGDSVTTDHISPAGAIPKDSPAAQFLRNHGIDEKDFNSYGSRRGNHEIMMRGTFGNIRI 723

Query: 727 RNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWAAKGTN 786
           RNEMTP +EGG T      + M I+DAAMRYQ+ ++  V+IAGKEYG GSSRDWAAKGT 
Sbjct: 724 RNEMTPDKEGGYTHLQGQSQAMFIFDAAMRYQQEKRSSVVIAGKEYGMGSSRDWAAKGTL 783

Query: 787 LLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISI-EISDKLTPGA 845
           LLG KAVI ESFERIHR+NL GMG+LPLQF  G  RK+L+L G E   I  +  ++    
Sbjct: 784 LLGAKAVIAESFERIHRANLAGMGVLPLQFMAGEDRKSLQLTGDESFDIMGLEGEMNANQ 843

Query: 846 MVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKISS 891
            +   I    G   KI+ L R+DTA E++YY+ GG+L YVL +I S
Sbjct: 844 TLDAVIHYPSGKQRKIQLLSRLDTAIEVDYYRAGGVLTYVLNRIVS 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: 2001
Number of extensions: 97
Number of successful extensions: 4
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: 891
Length adjustment: 43
Effective length of query: 848
Effective length of database: 848
Effective search space:   719104
Effective search space used:   719104
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