GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Cupriavidus basilensis 4G11

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 RR42_RS14490 RR42_RS14490 aconitate hydratase

Query= SwissProt::Q5SMF6
         (902 letters)



>FitnessBrowser__Cup4G11:RR42_RS14490
          Length = 901

 Score =  965 bits (2494), Expect = 0.0
 Identities = 503/905 (55%), Positives = 638/905 (70%), Gaps = 21/905 (2%)

Query: 3   NSFQTLKTLTTKSGTYG-YYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTRED 61
           N  +TLK       + G +Y L +L +     V RLP SIRV+LES+LRN DG +VT E 
Sbjct: 4   NLNKTLKEFKIGPSSKGQFYSLPQLGKALGVAVERLPVSIRVVLESVLRNCDGKKVTEEH 63

Query: 62  IEALARWRPDPGEIN-VPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVP 120
           +  LA W+P    ++ +P  +ARV+LQDFTGVP + DLAAMR+  +  G +PK+I P+VP
Sbjct: 64  VRQLAHWKPVAERVDEIPFVVARVVLQDFTGVPLLADLAAMRNVAEKMGKNPKKIEPLVP 123

Query: 121 ADLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQ 180
            DLV+DHSVQ+D F    A   N++ E++RN ERY  +KW   A + F VV PG GIVHQ
Sbjct: 124 VDLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQFMKWGMQAFDTFGVVQPGFGIVHQ 183

Query: 181 VNIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPY 240
           VN+EYL + V   K+DG+   +PD+LVGTDSHTTM+NG+GV+GWGVGGIEAEA MLGQP 
Sbjct: 184 VNLEYLARGVH--KKDGVY--YPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPV 239

Query: 241 YMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRAT 300
           Y L P VVG +L G L EG TATDLVLT+TEMLR+  VVGKFVEF+G G A L+ PDRAT
Sbjct: 240 YFLTPDVVGVELKGRLREGVTATDLVLTITEMLRREKVVGKFVEFFGEGTASLALPDRAT 299

Query: 301 IANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYS 360
           I NMAPEYGATMGFFPVDE+T++Y + TGR EE +   E Y +A  +F  P+A E + Y+
Sbjct: 300 IGNMAPEYGATMGFFPVDEKTIDYFKGTGRTEEEIAAFEGYFRAQKMFGVPKAGE-IDYT 358

Query: 361 EYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVK 420
             + LDL  V PSLAGPKRPQDR+ +  VK +F +   KP  E GF     +L +     
Sbjct: 359 NVVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTFASLFAKPTAENGFNKDIAELDKTYTTA 418

Query: 421 RRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSK 480
              +   +  G V+IAAITSCTNTSNPSV+L AGLLAKKAVEAGL   P +KTSLAPGS+
Sbjct: 419 ---DGVNVKSGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVAPHIKTSLAPGSR 475

Query: 481 VVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNR 540
           VVT+YL+ +GL+P+LE LGF +  YGCTTCIGN+G L  ++ +A+   +LV AAVLSGNR
Sbjct: 476 VVTEYLQAAGLLPYLEKLGFGVTAYGCTTCIGNAGDLTPELNEAITRNDLVAAAVLSGNR 535

Query: 541 NFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEI 600
           NFE RI+P+++AN+LASP LVVAYA+AG +  D  TEP+G    G+ IYL DIWP+ EEI
Sbjct: 536 NFEARIHPNIRANFLASPPLVVAYAIAGNVTRDLMTEPVGTGKGGREIYLGDIWPTSEEI 595

Query: 601 REAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGERK 660
              ++  +D ++FK  Y +V +  + W  +    G++Y W P+STYI  PPFF+  G   
Sbjct: 596 HALMKYAMDSKVFKINYEQVKKPSKLWAKVKGTKGQVYDW-PKSTYIAEPPFFDGFGMEP 654

Query: 661 V---EDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGN 717
                 +R AR L V GDSVTTDHISPAG+I   SPAG+YL++ GV   DFNSYGSRRGN
Sbjct: 655 AATQSSVRNARALGVFGDSVTTDHISPAGSIKESSPAGKYLLANGVLKADFNSYGSRRGN 714

Query: 718 HEVMMRGTFANIRIKNLML----DG--IEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLV 771
           HEVMMRGTFAN+RIKNLML    DG  +EGG     P G+   +Y+ AM+Y AEGTP +V
Sbjct: 715 HEVMMRGTFANVRIKNLMLPVKADGSRVEGGVTLHQPSGEALSIYDAAMKYIAEGTPTVV 774

Query: 772 IAGKEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLG 831
             G+EYGTGSSRDWAAKGT LLG++AV+  SFERIHRSNLVGMGVLPL+F   ++ +TLG
Sbjct: 775 FGGEEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGSDSVQTLG 834

Query: 832 LTGYEVYDILGLE-DLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTV 890
           + G E +DI G+E +LKP++ V +V +R +G   R   + R+DTP+EVDYY +GGIL  V
Sbjct: 835 IVGDETFDIEGIEGELKPQQDVTLVIKRANGDVQRVPLLLRIDTPIEVDYYNHGGILPFV 894

Query: 891 LLNML 895
           L  +L
Sbjct: 895 LRQLL 899


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: 2178
Number of extensions: 98
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: 901
Length adjustment: 43
Effective length of query: 859
Effective length of database: 858
Effective search space:   737022
Effective search space used:   737022
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