Alignments for a candidate for acn in Cupriavidus basilensis 4G11

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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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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