Alignments for a candidate for acn in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Dechlorosoma suillum PS

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 Dsui_2347 Dsui_2347 aconitate hydratase 1

Query= SwissProt::Q5SMF6
         (902 letters)



>FitnessBrowser__PS:Dsui_2347
          Length = 898

 Score =  987 bits (2552), Expect = 0.0
 Identities = 519/904 (57%), Positives = 653/904 (72%), Gaps = 21/904 (2%)

Query: 3   NSFQTLKTLTTKSGTYG-YYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTRED 61
           +SF TL+ L T  G  G ++ L  LE  G+  VSRLP S+R++LE+LLR+ DG +VT   
Sbjct: 4   DSFSTLQPLATAQGPIGLFHSLPALEAAGIGPVSRLPVSLRIVLEALLRHCDGRRVTPRH 63

Query: 62  IEALARWRPDPGEIN-VPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVP 120
           +  LA W+P       +P  +ARV+LQDFTGVP + DLAAMRDA  A+G DPKRI P+VP
Sbjct: 64  VLQLANWQPRAERTEEIPFVVARVVLQDFTGVPLLCDLAAMRDAAAAQGTDPKRIEPLVP 123

Query: 121 ADLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQ 180
            DLV+DHSVQVD +GT  A   N+E E++RN ERY  +KW   A + F+VVPPG GIVHQ
Sbjct: 124 VDLVVDHSVQVDEYGTPTALRRNMELEFQRNAERYQFMKWGMQAFDTFKVVPPGIGIVHQ 183

Query: 181 VNIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPY 240
           VN+EYL + V   +R G  L FPD+LVGTDSHTTM+NG+GV+GWGVGGIEAEA MLGQP 
Sbjct: 184 VNLEYLFRGV---RRQG-ELLFPDTLVGTDSHTTMINGVGVVGWGVGGIEAEAAMLGQPV 239

Query: 241 YMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRAT 300
           Y L P VVG +L G L EG TATDLVLTVTE+LR+  VVGKFVEF+GPG   LS  DRAT
Sbjct: 240 YFLTPDVVGVELRGRLNEGVTATDLVLTVTELLRREKVVGKFVEFFGPGSTSLSLTDRAT 299

Query: 301 IANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYS 360
           IANMAPEYGAT+GFFPVDE+T++YLRQTGR E  VE  EAY +A GLF  P A + + YS
Sbjct: 300 IANMAPEYGATLGFFPVDEKTVDYLRQTGRNEAEVEAFEAYFRAQGLFGAPRAGD-IDYS 358

Query: 361 EYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVK 420
             L LDL+ + PSLAGPKRPQDR+ L ++ +SF    ++P    GFG   +QL ++    
Sbjct: 359 TQLSLDLATIVPSLAGPKRPQDRIDLSDMGRSFDTLFSQPTSANGFGKPAEQLPQRQPTA 418

Query: 421 RRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSK 480
           R     +L HG V+IAAITSCTNTSNP+V++ AGLLAKKAV+ GL  +P +KTSLAPGS+
Sbjct: 419 RAG--VDLGHGDVLIAAITSCTNTSNPAVLIAAGLLAKKAVDKGLSVQPHIKTSLAPGSR 476

Query: 481 VVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNR 540
           VVTDYLE +GL+  L  LGF L GYGCTTCIGN+G L  +  +A+ E +LVVAAVLSGNR
Sbjct: 477 VVTDYLEKAGLLAPLARLGFALAGYGCTTCIGNAGDLAPEFNQAIAERDLVVAAVLSGNR 536

Query: 541 NFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEI 600
           NFE RI+P ++ANYLASP LVVA+A+AGR+++D TT PLG   +G+P+YL++IWPS EEI
Sbjct: 537 NFEARIHPAIRANYLASPPLVVAFAIAGRVNVDLTTTPLGTGRDGQPVYLREIWPSSEEI 596

Query: 601 REAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFE--DLGE 658
              +    DP  +++ Y+      + W A+PAP G++Y W P STYI  PPFF+   +  
Sbjct: 597 ATVLPFAQDPATYRRLYADFTRDHDLWNAVPAPEGQIYDW-PPSTYIARPPFFDGFTVEP 655

Query: 659 RKVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGNH 718
             +  I GAR LLVLGDSVTTDHISPAG+    +PAGQ+L ++GVK  DFNSYGSRRG+H
Sbjct: 656 PPLAPINGARALLVLGDSVTTDHISPAGSFKAATPAGQWLTAQGVKSLDFNSYGSRRGHH 715

Query: 719 EVMMRGTFANIRIKNLML----DG--IEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVI 772
           EVM+RGTFAN+R+KNLML    DG  +EGGY   L +G    V+  A  Y+  G P LV 
Sbjct: 716 EVMVRGTFANVRVKNLMLPPKADGSPVEGGYT--LLDGQQVTVFEAASAYQQRGIPTLVF 773

Query: 773 AGKEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGL 832
           AG+EYGTGSSRDWAAKGT LLG+RAV+A SFERIHR+NLVGMGVLPL+F  G +  +LGL
Sbjct: 774 AGEEYGTGSSRDWAAKGTRLLGVRAVVARSFERIHRANLVGMGVLPLQFKAGTSAASLGL 833

Query: 833 TGYEVYDILGLE-DLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVL 891
            G E +D+ G +  L+ ++ + +   R DG   +   + R+DTP+EV+Y+++GGIL  VL
Sbjct: 834 DGSEHFDLPGADGPLQAQQDLMLRITRSDGRVEQVPLLCRIDTPIEVEYFRHGGILPYVL 893

Query: 892 LNML 895
             +L
Sbjct: 894 RQLL 897


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: 2190
Number of extensions: 101
Number of successful extensions: 9
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: 898
Length adjustment: 43
Effective length of query: 859
Effective length of database: 855
Effective search space:   734445
Effective search space used:   734445
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