Alignments for a candidate for acn in Halomonas stevensii S18214

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Halomonas stevensii S18214

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_016916040.1 HSS18214_RS0114705 aconitate hydratase AcnA

Query= SwissProt::P37032
         (891 letters)



>NCBI__GCF_000275725.1:WP_016916040.1
          Length = 915

 Score = 1169 bits (3025), Expect = 0.0
 Identities = 594/910 (65%), Positives = 700/910 (76%), Gaps = 33/910 (3%)

Query: 9   STKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTKDIKAI 68
           ST   LT   + Y+YYSL +A       I+RLP +LK+LLEN LRF D  +V   D++A+
Sbjct: 6   STLHTLTAGSQEYHYYSLPKAAET-LGNIDRLPKTLKILLENQLRFADDESVEQADMQAL 64

Query: 69  ADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLSPVDLV 128
            DW +   S  EI +RP RVLMQDFTGVP VVDLA+MR A+  +G +  +I+PLSPVDLV
Sbjct: 65  VDWQNEGQSSREIGYRPARVLMQDFTGVPGVVDLASMRAAVESLGEDPARINPLSPVDLV 124

Query: 129 IDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICHQVNLE 188
           IDHSVMVDKF +  A + N  IE++RN ERYEFLRWGQKAF NF VVPPGTGICHQVNLE
Sbjct: 125 IDHSVMVDKFGTPTAFQENVDIEMQRNGERYEFLRWGQKAFDNFSVVPPGTGICHQVNLE 184

Query: 189 YLGKTVWNSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLI 248
           YLG+TVW  + DG+ +AYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLI
Sbjct: 185 YLGRTVWTKQEDGKTFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLI 244

Query: 249 PEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADRATISNM 308
           PEVIGFKL+GKL+EGITATDLVLTVT+MLRKKGVVGKFVEFYG GL DLPLADRATI+NM
Sbjct: 245 PEVIGFKLTGKLQEGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDLPLADRATIANM 304

Query: 309 APEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVFTDSLHL 368
           APEYGATCGFFPVD ET+ YL LTGR+   +ALVEAY+KAQG+W +   +EP+FTD+L L
Sbjct: 305 APEYGATCGFFPVDDETLNYLRLTGREDELVALVEAYSKAQGLWRE-PGDEPIFTDTLSL 363

Query: 369 DLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGK---------------------EK 407
           D+ SVE SLAGPKRPQD+V+L ++P  F + + E GK                     ++
Sbjct: 364 DMSSVEASLAGPKRPQDRVSLKNMPKAFASVMEEDGKSYPATETGKLSSEGGQTAVGIDR 423

Query: 408 EKEKTF------AVK--NKDFQMKHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGL 459
             E+ F      AVK   +DF +  G VVIAAITSCTNTSNPSV+MAAGL+A+ A +KGL
Sbjct: 424 SFERAFQHNDSQAVKMGEQDFNLDPGAVVIAAITSCTNTSNPSVMMAAGLLARNARQKGL 483

Query: 460 QRKPWVKSSLAPGSKVVTDYLRHAGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCV 519
             KPWVK+SLAPGSKVVTDYL  A L   LD LGFNLVGYGCTTCIGNSGPLPD I   +
Sbjct: 484 ATKPWVKTSLAPGSKVVTDYLAAAELNDDLDALGFNLVGYGCTTCIGNSGPLPDAIEKAI 543

Query: 520 AEHDLVVSSVLSGNRNFEGRVHPQVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEG 579
            + DL V+SVLSGNRNFEGRVHP V+ NWLASPPLVVAYAL G    +LS +P+G+D +G
Sbjct: 544 QQGDLAVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVQCNLSTDPLGEDSDG 603

Query: 580 NDVYLKDIWPSNEEIAAEVAKVSGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTY 639
           N VYLKDIWPS  +IA  V KV+  MFRKEY+ VF+GD  WQ+I+      YEW P STY
Sbjct: 604 NPVYLKDIWPSQADIANAVQKVNTEMFRKEYSAVFEGDETWQSIKVPESNVYEW-PSSTY 662

Query: 640 IQHPPFFENLSLKPEPLKPIKQAYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVD 699
           IQHPPFF+ +  +P+ ++ I+ A VLA+ GDS+TTDHISPAGSIK  SPAG YL+  GV 
Sbjct: 663 IQHPPFFKGMQREPDAIEDIQSARVLAILGDSVTTDHISPAGSIKPDSPAGRYLQEHGVK 722

Query: 700 EKDFNSYGSRRGNHEVMMRGTFANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQE 759
             DFNSYGSRRGNHEVMMRGTFAN+RI+NEM  G  GG TR+VP+GE MSIYDAAM+Y+E
Sbjct: 723 PVDFNSYGSRRGNHEVMMRGTFANVRIKNEMLDGVVGGETRHVPSGEQMSIYDAAMKYKE 782

Query: 760 NQQDLVIIAGKEYGTGSSRDWAAKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEG 819
               LV++AGKEYGTGSSRDWAAKGT LLGV+AVI ES+ERIHRSNLIGMG++PLQF EG
Sbjct: 783 EGTPLVVVAGKEYGTGSSRDWAAKGTRLLGVRAVIAESYERIHRSNLIGMGVVPLQFPEG 842

Query: 820 TTRKTLKLDGSERISIEISDKLTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNG 879
            +R +L L G E ISI   + L+PG  V V I++ D +   ++  CRIDTA+EL YY++G
Sbjct: 843 ESRTSLGLTGDEEISIAGLNDLSPGGTVKVVIKQGDQE-RTVDAKCRIDTANELAYYRHG 901

Query: 880 GILQYVLRKI 889
           GIL YVLRK+
Sbjct: 902 GILHYVLRKM 911


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: 2143
Number of extensions: 97
Number of successful extensions: 6
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: 915
Length adjustment: 43
Effective length of query: 848
Effective length of database: 872
Effective search space:   739456
Effective search space used:   739456
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