Alignments for a candidate for acn in Sinorhizobium medicae WSM419

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Sinorhizobium medicae WSM419

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_011974570.1 SMED_RS01825 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_000017145.1:WP_011974570.1
          Length = 872

 Score =  763 bits (1969), Expect = 0.0
 Identities = 414/880 (47%), Positives = 560/880 (63%), Gaps = 33/880 (3%)

Query: 21  YDLQELERKGVAEVSRLPFSIRVMLESLLRN--EDGYQVTREDIEALARWRPDPGEINVP 78
           YD+ +L  +   ++  LP+  R++LE++LR   ED  +     I+ LA       E+ + 
Sbjct: 14  YDVIDLPAEVGHQLRSLPYIHRILLENVLRTAGEDAARAKAAIIDWLAT---GSSELEIQ 70

Query: 79  LKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPADLVIDHSVQVDAFGTAY 138
               RV++ D T  PA+VD+A MR A+   G DP  +NPVVP D+  DHS+ VD FG + 
Sbjct: 71  FLPNRVMMHDTTCGPALVDIAGMRSALAEAGYDPALLNPVVPVDVSTDHSLAVDVFGHSA 130

Query: 139 AFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVNIEYLTKVVMTGKRDGL 198
           +   N+++E+ERN ERY  +KWA N L  FRV PPGTGI+H +N+E L  VV T ++DG 
Sbjct: 131 SLELNMKREFERNAERYRFMKWATNTLTGFRVHPPGTGIMHTLNLERLATVVSTLEKDGR 190

Query: 199 TLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYYMLAPRVVGFKLYGELPE 258
             A PD+L+GTDSHT M+NG+GVL WGVGG+EAE+V  G P  +  P VVG +L G L +
Sbjct: 191 RWAAPDTLIGTDSHTPMINGIGVLAWGVGGLEAESVFFGMPVSLRVPDVVGVRLTGRLGD 250

Query: 259 GATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATIANMAPEYGATMGFFPVD 318
           G  ATDL LTVT +LRK  +  K+VEFYGPGV+ L+  DR+ +ANM PE+G   G+FPVD
Sbjct: 251 GVLATDLALTVTHILRKIDLQDKYVEFYGPGVSLLTAGDRSVVANMTPEFGGNSGYFPVD 310

Query: 319 EETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSEYLELDLSAVEPSLAGPK 378
             TL+YLR TGR  E VELVEA+TK VGL+  P  +EK +Y+  +E+DLSA+EPSLAGP 
Sbjct: 311 GRTLDYLRTTGRTSEQVELVEAFTKRVGLWFDP--DEKPRYTHVVEIDLSAIEPSLAGPT 368

Query: 379 RPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVKRRDEEFELTHGSVVIAAI 438
           RP DR+ + E   +                    ++R  +V       E   G+V IAAI
Sbjct: 369 RPHDRISVGETSAAI-----------------SSMKRDAVVSAHTS--EPNDGAVAIAAI 409

Query: 439 TSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSKVVTDYLEMSGLMPFLEAL 498
           TSCTNTS+P +++ AGLLA+KA   GL   PWVKTSLAPGS     YL  SGL+  LEA+
Sbjct: 410 TSCTNTSDPRLVIAAGLLARKARALGLHPAPWVKTSLAPGSPTAERYLRRSGLLQDLEAV 469

Query: 499 GFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNRNFEGRINPHVKANYLASP 558
           GF +VGYGCTTCIGNSGPL E IA A+++  ++  AVLSGNRNF GR++P ++A +LASP
Sbjct: 470 GFGIVGYGCTTCIGNSGPLTEPIAVAMKDRGILPVAVLSGNRNFPGRVHPQLEAGFLASP 529

Query: 559 MLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEIREAIRKTLDPELFKKEYS 618
            LVVA+ALAG ++++  T+ +G   +G+ + L  +WP+ +EI EA+    D   FK+ Y 
Sbjct: 530 PLVVAFALAGTVELNILTDVIGRSSDGQAVTLSMLWPTSQEIDEAVTLAADAMDFKRAYD 589

Query: 619 KVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGERKVEDIRGARVLLVLGDSVT 678
           +  E  + W+ L APT  L+ WD  STYI+ PP F   G+  +     A  L+V+GD +T
Sbjct: 590 EA-EASKAWRELEAPTTTLFPWDETSTYIRRPP-FAGFGKGSLLGTYDAHPLIVVGDDIT 647

Query: 679 TDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGNHEVMMRGTFANIRIKNLMLDG 738
           TDHISPAGAI  +S  G+YL+  G  P D N + SRRGN E M+RG + N  ++N +   
Sbjct: 648 TDHISPAGAIRAQSETGRYLVELGEVPTDLNVHASRRGNWESMVRGLYTNRTVQNFLGVE 707

Query: 739 IEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGKEYGTGSSRDWAAKGTYLLGIRAV 798
           I  G     P G++  +++ A RY      ++++AG+ YG GSSRDWAAKG  LLG RAV
Sbjct: 708 IPPGSTIHAPSGELLPLWSAANRYAESKQSVVIVAGERYGMGSSRDWAAKGASLLGARAV 767

Query: 799 LAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGYEVYDI---LGLEDLKPRKLVDIV 855
           LA SFERIHRSNL+GMGVLP+    G   + L L   ++ +I    GL  + PR  +D+V
Sbjct: 768 LAVSFERIHRSNLIGMGVLPMRLPEGLGPDELALRSGDLIEIHADAGL--IAPRCPIDVV 825

Query: 856 ARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNML 895
            RR DG   RF+A   ++T  EV+  K GGIL  +L N++
Sbjct: 826 IRRRDGEITRFRATTAIETVAEVEMLKAGGILPLMLKNLV 865


Lambda     K      H
   0.317    0.137    0.399 

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: 1903
Number of extensions: 79
Number of successful extensions: 7
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: 902
Length of database: 872
Length adjustment: 43
Effective length of query: 859
Effective length of database: 829
Effective search space:   712111
Effective search space used:   712111
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