GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_4039 Echvi_4039 aconitate hydratase 1

Query= SwissProt::Q5SMF6
         (902 letters)



>FitnessBrowser__Cola:Echvi_4039
          Length = 925

 Score = 1047 bits (2707), Expect = 0.0
 Identities = 539/923 (58%), Positives = 682/923 (73%), Gaps = 42/923 (4%)

Query: 9   KTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDIEALARW 68
           K L T  G+  Y+ L  L+ +G  +++ LPFSIR++LE+ LRN D + +T+E  E L  W
Sbjct: 10  KQLDTAKGSLNYWSLAALQEQG-HKINELPFSIRILLENALRNYDDFAITKEHTETLLNW 68

Query: 69  RPDPGEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPADLVIDHS 128
           +P+  + +VP K ARV++QDFTGVPAVVD+A++R     KG DP++INP++P DLV+DHS
Sbjct: 69  KPEASDKDVPYKPARVLMQDFTGVPAVVDIASLRAEAVRKGKDPQKINPLIPVDLVVDHS 128

Query: 129 VQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVNIEYLTK 188
           VQVD FGT Y++  NV+ EYERN ERY  LKWAQ + +NF VVPPG GI HQVN+EYL K
Sbjct: 129 VQVDYFGTNYSYKKNVDVEYERNGERYEFLKWAQKSFDNFSVVPPGMGICHQVNLEYLAK 188

Query: 189 VVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYYMLAPRVV 248
            V+  +RDG    FPD+LVGTDSHT MVNG+GV+GWGVGGIEAEA +LGQP Y + P+VV
Sbjct: 189 GVI--ERDGNV--FPDTLVGTDSHTPMVNGIGVVGWGVGGIEAEAALLGQPIYFIMPQVV 244

Query: 249 GFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATIANMAPEY 308
           G KL GELP G TATD+VLT+TE+LRKHGVVGKFVE +GPG+  L+ PDRATI+NM+PE+
Sbjct: 245 GLKLTGELPLGTTATDMVLTITELLRKHGVVGKFVEVFGPGLDTLTVPDRATISNMSPEF 304

Query: 309 GATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSEYLELDLS 368
           G T+ +FP+D+ TL+Y+ +T R ++ ++LVE Y KA  L+R  E EE V+YS  +ELDL 
Sbjct: 305 GCTVTYFPIDDRTLDYMSKTNRSKDQIKLVEDYAKANMLWR--EDEESVKYSSLVELDLG 362

Query: 369 AVEPSLAGPKRPQDRVPLKEVKKSF-----------LAHLTKPVKERGFG---------- 407
            VEP+++GPKRPQD++ ++  K+ F              + K  K R F           
Sbjct: 363 TVEPTVSGPKRPQDKILVRNFKEKFGELLEEVHGREYIPIDKRDKSRWFSEGGGQPVDKP 422

Query: 408 --LSED-QLQRK-------VLVKRRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLA 457
             L ED ++  K       V VK  +EEF L+ GS+VIAAITSCTNTSNPSVM+GAGL+A
Sbjct: 423 GDLPEDVEIATKTKNGLKTVEVKINNEEFALSDGSIVIAAITSCTNTSNPSVMIGAGLVA 482

Query: 458 KKAVEAGLDRKPWVKTSLAPGSKVVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPL 517
           +KA E GLD KPWVKTSLAPGSKVVTDYLE SGL+  LEAL FH+VGYGCT+CIGNSGPL
Sbjct: 483 QKARERGLDVKPWVKTSLAPGSKVVTDYLEASGLLDDLEALRFHVVGYGCTSCIGNSGPL 542

Query: 518 PEDIAKAVEEGNLVVAAVLSGNRNFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTE 577
           P+ IA AVEE +LVVA+VLSGNRNFE R++P VK NYL SPMLVVAYALAGR+D+D   E
Sbjct: 543 PKHIAHAVEENDLVVASVLSGNRNFEARVHPQVKMNYLMSPMLVVAYALAGRVDVDLNEE 602

Query: 578 PLGFDPNGKPIYLKDIWPSMEEIREAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGEL 637
           PLGFDPN +P+YLKDIWPS +EI E + K L P  F K Y ++FEG+E+W+ L AP+ ++
Sbjct: 603 PLGFDPNLEPVYLKDIWPSNDEIFEVMGKVLSPGDFDKNYGEIFEGNEQWKNLQAPSDKV 662

Query: 638 YQWDPESTYIQNPPFFEDLGER--KVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAG 695
           Y W  +STYI+  PFF+ L     + ++I+GARVLL LGDS+TTDHISPAGA    SPAG
Sbjct: 663 YNWSEKSTYIKEAPFFQGLSNEVPEPQNIQGARVLLKLGDSITTDHISPAGAFAESSPAG 722

Query: 696 QYLISKGVKPEDFNSYGSRRGNHEVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFV 755
           QYL+ +GV+ +DFNSYGSRRGN EVM+RGTFAN+RIKN  L   EGGY   +P G+   V
Sbjct: 723 QYLVGRGVEKKDFNSYGSRRGNDEVMVRGTFANVRIKN-QLASREGGYTTHIPSGEEMTV 781

Query: 756 YNVAMRYKAEGTPLLVIAGKEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMG 815
           +  + +Y+ + TPL+V+AGKEYG+GSSRDWAAKGT LLGI AV+AES+ERIHRSNLVGMG
Sbjct: 782 FEASEKYQKDDTPLVVLAGKEYGSGSSRDWAAKGTTLLGIHAVIAESYERIHRSNLVGMG 841

Query: 816 VLPLEFLPGENRETLGLTGYEVYDILGL-EDLKPRKLVDIVARREDGSEVRFQAIARLDT 874
           VLPL+F  G++  +LGL G E   I G+ E L P K +   A+++ G+ V F  + RLD+
Sbjct: 842 VLPLQFAEGQSASSLGLDGKEEITIEGITEGLTPLKNLKATAKKDGGAVVNFDVVCRLDS 901

Query: 875 PVEVDYYKNGGILQTVLLNMLKE 897
            VE+ YYKNGGIL  VL   LK+
Sbjct: 902 EVEIAYYKNGGILHYVLREFLKQ 924


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: 2285
Number of extensions: 107
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 902
Length of database: 925
Length adjustment: 43
Effective length of query: 859
Effective length of database: 882
Effective search space:   757638
Effective search space used:   757638
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