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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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