Alignments for a candidate for acn in Psychrobacter arcticus 273-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Psychrobacter arcticus 273-4

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_011281315.1 PSYC_RS10685 aconitate hydratase AcnA

Query= SwissProt::P37032
         (891 letters)



>NCBI__GCF_000012305.1:WP_011281315.1
          Length = 939

 Score = 1045 bits (2701), Expect = 0.0
 Identities = 536/933 (57%), Positives = 668/933 (71%), Gaps = 49/933 (5%)

Query: 6   DSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFED-GNTVTTKD 64
           D  + K  + VDGK Y YYSL +    H + I++LP+ +KV+LENLLR ED G +V    
Sbjct: 3   DIFNVKDTIAVDGKEYAYYSLPKLTETH-ENISKLPFCMKVVLENLLRNEDDGQSVGKNH 61

Query: 65  IKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLSP 124
           I+A+A+W     +  EIAF P RV++QDFTGVP+VVDLAAMR A+V++GGNA++I+P  P
Sbjct: 62  IEAVANWDAGAEASKEIAFMPARVVLQDFTGVPSVVDLAAMRDAVVELGGNAEQINPFIP 121

Query: 125 VDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICHQ 184
            +LV+DHSV VD +   DAL++N KIE +RN ERYEFL WG+ AF NF VVPP TGI HQ
Sbjct: 122 SELVVDHSVQVDAYGREDALDLNEKIEFKRNNERYEFLHWGRNAFKNFVVVPPATGIVHQ 181

Query: 185 VNLEYLGKTVWNSENDG----QLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAML 240
           VNLEYL + V  ++ D     +L AYPDT+ GTDSHTTMING+GVLGWGVGGIEAEAAML
Sbjct: 182 VNLEYLARVVMAADVDNGDGVELTAYPDTVFGTDSHTTMINGIGVLGWGVGGIEAEAAML 241

Query: 241 GQPVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLA 300
           GQP SMLIP+V+GF+L GKL EG+TATDLVL V +MLR  GVVGKFVEFYG GL+ +PLA
Sbjct: 242 GQPSSMLIPQVVGFELKGKLTEGVTATDLVLRVVEMLRAHGVVGKFVEFYGEGLHSMPLA 301

Query: 301 DRATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEP 360
           DRATI+NM+PEYGATCG FP+D+  I YL L+GRD+  I LVE YAKAQG+W+D D    
Sbjct: 302 DRATIANMSPEYGATCGIFPIDQMAIDYLRLSGRDEAQIELVEKYAKAQGLWHDADTPAA 361

Query: 361 VFTDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLI-----------------EV 403
            ++  L LDL SV+P+LAGP  PQ ++NLS +  +F   L                  + 
Sbjct: 362 TYSSKLELDLSSVQPALAGPNLPQQRINLSDMHKKFGETLTAMTKDRKSEVEGKVRFDQE 421

Query: 404 GKEKEKEKTFAVK-----------------NKDFQMKHGHVVIAAITSCTNTSNPSVLMA 446
           G E+E+ KT A K                 ++++ ++ G VVIAAITSCTNTSNP+V++ 
Sbjct: 422 GGEQEQAKTLAAKPNPFCAEGSTYCTVKIEDEEYSLRDGSVVIAAITSCTNTSNPAVMIG 481

Query: 447 AGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRHAGLQTYLDQLGFNLVGYGCTTCIG 506
           AGLVAKKA  KGL  KPWVK+SLAPGSKVVTDYL  A L   L+++GF LVGYGCTTCIG
Sbjct: 482 AGLVAKKAAAKGLTAKPWVKTSLAPGSKVVTDYLEKAKLMDELEKIGFYLVGYGCTTCIG 541

Query: 507 NSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHPQVRANWLASPPLVVAYALCGTTCS 566
           NSGPL   I   + E DLV ++VLSGNRNFEGR+H  V+A++LASPPLVVAYAL GT   
Sbjct: 542 NSGPLLGAIEGAIEEGDLVAAAVLSGNRNFEGRIHSHVKASYLASPPLVVAYALAGTVDI 601

Query: 567 DLSREPIGQDKEGNDVYLKDIWPSNEEIAAEVA-KVSGTMFRKEYAEVFKGDAHWQAIQT 625
           DL+  P+GQD+EGNDVYLKDIWP+++EI   +A  +   MFRK Y EVF G A W AI +
Sbjct: 602 DLTTHPLGQDQEGNDVYLKDIWPTSDEINELIANNIDADMFRKNYGEVFDGSAAWNAISS 661

Query: 626 SSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQAYVLALFGDSITTDHISPAGSIKA 685
           +  Q Y W+ +STYI++PPFF+ ++++PE +  I+ A +L LFGDSITTDHISPAG+I A
Sbjct: 662 ADSQLYPWSEESTYIKNPPFFDGMTMEPEGIPDIEGARILGLFGDSITTDHISPAGNIDA 721

Query: 686 SSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTFANIRIRNEMTPGQEGGVTRY---- 741
            SPAG YL+ +GV E DFNSYGSRRGN  VM RGTFANIRI+N M  G+EGG T Y    
Sbjct: 722 DSPAGKYLQERGVMEADFNSYGSRRGNDAVMTRGTFANIRIKNTMMGGKEGGYTYYFNGD 781

Query: 742 ---VPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWAAKGTNLLGVKAVITESF 798
              +  GE M+IYDAAM+Y+E+++ LV++ G EYG+GSSRDWAAKGT LLGVKAV+T SF
Sbjct: 782 SATLQDGEEMAIYDAAMKYKEDKRPLVVLGGAEYGSGSSRDWAAKGTILLGVKAVLTSSF 841

Query: 799 ERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIEISDKLTPGAMVPVTIERQDGDI 858
           ERIHRSNL+GMG+LPL FK G    T  LDGSE +SI   D         VT  R DG  
Sbjct: 842 ERIHRSNLVGMGVLPLTFKAGENAATYNLDGSEVLSITGLDN-GESKTAKVTATRADGST 900

Query: 859 EKIETLCRIDTADELEYYKNGGILQYVLRKISS 891
           E  +    + T  E EY ++GG+L YVLR++++
Sbjct: 901 ESFDVNVMLQTPKEREYVRHGGVLHYVLRQLAA 933


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: 2097
Number of extensions: 102
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: 939
Length adjustment: 43
Effective length of query: 848
Effective length of database: 896
Effective search space:   759808
Effective search space used:   759808
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