Alignments for a candidate for acn in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Halomonas desiderata SP1

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_086509356.1 BZY95_RS07660 aconitate hydratase AcnA

Query= SwissProt::P37032
         (891 letters)



>NCBI__GCF_002151265.1:WP_086509356.1
          Length = 916

 Score = 1196 bits (3093), Expect = 0.0
 Identities = 598/907 (65%), Positives = 705/907 (77%), Gaps = 30/907 (3%)

Query: 10  TKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTKDIKAIA 69
           T   L  DG TY+YYSL +   +    I+RLP +LK+LLEN LRF D  +V  +DI+A+ 
Sbjct: 9   TLQTLVADGTTYHYYSLPKVAEE-MGNIDRLPKTLKILLENQLRFADDPSVAREDIQALI 67

Query: 70  DWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLSPVDLVI 129
           DW     S  EI +RP RVLMQDFTGVP VVDLA+MR A+ K+G +  +I+PLSPVDLVI
Sbjct: 68  DWQQGGRSNREIGYRPARVLMQDFTGVPGVVDLASMRAAVEKLGEDPSRINPLSPVDLVI 127

Query: 130 DHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICHQVNLEY 189
           DHSVMVDKF +  A + N  IE+ERN+ERYEFLRWGQ+AF NF VVPPGTGICHQVNLEY
Sbjct: 128 DHSVMVDKFGNPTAFKDNVAIEMERNRERYEFLRWGQQAFDNFSVVPPGTGICHQVNLEY 187

Query: 190 LGKTVWNSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP 249
           LG+TVW  E +G+++AYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP
Sbjct: 188 LGRTVWTKEENGKVFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP 247

Query: 250 EVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADRATISNMA 309
           EV+GFKL+GKLKEGITATDLVLTVTQMLR +GVVGKFVEFYG GL DLPLADRATI+NMA
Sbjct: 248 EVVGFKLTGKLKEGITATDLVLTVTQMLRSRGVVGKFVEFYGDGLADLPLADRATIANMA 307

Query: 310 PEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVFTDSLHLD 369
           PEYGATCGFFPVD ET+ YL LTGR+   IALV+ Y KAQG+W +   +EP+F+D+LHLD
Sbjct: 308 PEYGATCGFFPVDDETLAYLRLTGREDSLIALVKEYCKAQGLWREP-GDEPIFSDTLHLD 366

Query: 370 LGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLI--EVGK---EKEKEKTFA---------- 414
           LG VE SLAGPKRPQD+V L  +   F   +   E GK    +EK + F+          
Sbjct: 367 LGDVEASLAGPKRPQDRVALKDMKTTFEKLMQGEENGKATPSEEKGRLFSEGGQTAVGVH 426

Query: 415 ------------VKNKDFQMKHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRK 462
                       +  + F++  G VVIAAITSCTNTSNPSV++AAGL+A+ A  KGL  K
Sbjct: 427 DSYEHHDSQNVEMDGEQFKLNPGAVVIAAITSCTNTSNPSVMLAAGLLARNARAKGLTTK 486

Query: 463 PWVKSSLAPGSKVVTDYLRHAGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEH 522
           PWVK+SLAPGSKVVT+YL    +Q  LD LGFNLVGYGCTTCIGNSGPLP  I   V + 
Sbjct: 487 PWVKTSLAPGSKVVTEYLAAGSVQDDLDALGFNLVGYGCTTCIGNSGPLPPPIEKAVEDG 546

Query: 523 DLVVSSVLSGNRNFEGRVHPQVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDV 582
           DL V+SVLSGNRNFEGR+HP V+ NWLASPPLVVAYAL G    DL+++P+G+D++GN V
Sbjct: 547 DLTVASVLSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNVRLDLTQDPLGEDQDGNPV 606

Query: 583 YLKDIWPSNEEIAAEVAKVSGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQH 642
           YL+DIWPS  +IA+ V KV   MFRKEYAEVF+GD  W+A+Q    Q YEW+P STYIQH
Sbjct: 607 YLQDIWPSQADIASAVEKVKTEMFRKEYAEVFEGDETWKALQVPQSQVYEWSPSSTYIQH 666

Query: 643 PPFFENLSLKPEPLKPIKQAYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKD 702
           PPFFE +   PEP++ ++ A++LA+ GDS+TTDHISPAGSIK  SPAG YL+ +G+   D
Sbjct: 667 PPFFEGMGRDPEPIEDVRDAHILAILGDSVTTDHISPAGSIKPDSPAGRYLQERGIKPVD 726

Query: 703 FNSYGSRRGNHEVMMRGTFANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQ 762
           FNSYGSRRGNHEVMMRGTFAN+RIRNEM  G  GG TR+VPTGE M+IYDAAM+YQE   
Sbjct: 727 FNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVVGGETRHVPTGEQMAIYDAAMKYQEKGT 786

Query: 763 DLVIIAGKEYGTGSSRDWAAKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTR 822
            LV++AGKEYGTGSSRDWAAKGT LLGV+AV+ ES+ERIHRSNLIGMG++PLQF EG  R
Sbjct: 787 PLVVVAGKEYGTGSSRDWAAKGTRLLGVRAVLAESYERIHRSNLIGMGVVPLQFPEGENR 846

Query: 823 KTLKLDGSERISIEISDKLTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGIL 882
           KTL L G E ISIE    LTPG  V VT++   G+ +KIE LCRIDTA+ELEYY++GGIL
Sbjct: 847 KTLGLTGDETISIEGLADLTPGGQVNVTVKSAKGE-KKIEALCRIDTANELEYYRHGGIL 905

Query: 883 QYVLRKI 889
            YVLR++
Sbjct: 906 HYVLRRM 912


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: 2199
Number of extensions: 87
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 891
Length of database: 916
Length adjustment: 43
Effective length of query: 848
Effective length of database: 873
Effective search space:   740304
Effective search space used:   740304
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