Alignments for a candidate for acn in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Derxia gummosa DSM 723

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 WP_028313040.1 H566_RS0121365 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_000482785.1:WP_028313040.1
          Length = 901

 Score =  985 bits (2547), Expect = 0.0
 Identities = 511/905 (56%), Positives = 642/905 (70%), Gaps = 19/905 (2%)

Query: 2   KNSFQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTRED 61
           K  F TLK          ++ L  LE+     VSRLP SIR++LES+LRN DG +VT E 
Sbjct: 3   KTPFNTLKNFKIGEKVAKFHSLPALEKTLGLPVSRLPVSIRIVLESVLRNCDGRKVTEEH 62

Query: 62  IEALARWRPD-PGEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVP 120
           +  LA W+P+ P    +P  +ARV+LQDFTGVP + DLAAMR+     G DPK I P+VP
Sbjct: 63  VRQLAAWQPNAPRTEEIPFVVARVVLQDFTGVPLLADLAAMRNVAADLGHDPKTIEPLVP 122

Query: 121 ADLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQ 180
            DLV+DHSV +D +G+  A   N++ E+ERNRERY  +KW   A ++F VVPPG GIVHQ
Sbjct: 123 VDLVVDHSVMIDHYGSKKALDLNMKLEFERNRERYQFMKWGMQAFDSFSVVPPGFGIVHQ 182

Query: 181 VNIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPY 240
           VN+EYL + V  G   G  + +PDSLVGTDSHTTM+NG+GV+GWGVGGIEAEA MLGQP 
Sbjct: 183 VNLEYLARGVHKG---GDGVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPV 239

Query: 241 YMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRAT 300
           Y L P VVGF+L G+L EG TATDLVLT+TE LR+  VVGKFVEF+GPG A LS PDRAT
Sbjct: 240 YFLTPDVVGFELTGKLREGVTATDLVLTITEQLRREKVVGKFVEFFGPGTASLSVPDRAT 299

Query: 301 IANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYS 360
           I NMAPEYGATMGFFPVDE+T+ Y R TGR +  +   E Y +A  LF  P A + + Y+
Sbjct: 300 IGNMAPEYGATMGFFPVDEKTVEYFRGTGRTKGEIAAFEGYFRAQKLFGVPMAGD-IDYT 358

Query: 361 EYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVK 420
           + + LDL  V PSLAGPKRPQDR+ +  +  SF    +KPV E GF    D+L +     
Sbjct: 359 KVVTLDLGTVTPSLAGPKRPQDRIEITNLSSSFSELFSKPVSENGFNQPADKLGQTFTT- 417

Query: 421 RRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSK 480
             D+   L +G V+IAAITSCTNTSNPSV+L AGLLAKKAVEAGL  K  VKTSLAPGS+
Sbjct: 418 --DDGIALRNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVKKHVKTSLAPGSR 475

Query: 481 VVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNR 540
           +VT+YL+ +GL+P+L  LGF +  YGCTTCIGN+G L  +I KA+ + +LVVAAVLSGNR
Sbjct: 476 IVTEYLDKAGLLPWLSKLGFDVAAYGCTTCIGNAGDLTPEINKAIIDNDLVVAAVLSGNR 535

Query: 541 NFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEI 600
           NFE RI+P++KAN+LASP LVVAYA+AG + +D  T+P+G    GKP+YL DIWP+ +EI
Sbjct: 536 NFEARIHPNIKANFLASPPLVVAYAIAGNVTVDLMTQPVGKGKGGKPVYLGDIWPTSDEI 595

Query: 601 REAIRKTLDPELFKKEYSKV-FEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLG-- 657
              ++  ++ + F+  Y+KV  E  + W+ +   +G++Y W P STYI  PPFF+  G  
Sbjct: 596 ARLMKYAMNGKAFRDNYAKVDAEPGKLWEKISGTSGQVYDW-PASTYIAKPPFFDSFGMA 654

Query: 658 -ERKVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRG 716
            E     IRGARV+ + GDS+TTDHISPAG+I   SP GQYL+  GV   DFNSYGSRRG
Sbjct: 655 PEAAASAIRGARVMALFGDSITTDHISPAGSIKEASPGGQYLVGNGVMKADFNSYGSRRG 714

Query: 717 NHEVMMRGTFANIRIKNLML----DGI--EGGYAKKLPEGDVDFVYNVAMRYKAEGTPLL 770
           NHEVMMRGTFAN+RIKNLM+    DG   EGG     P G+  F+Y+ AM+Y AEGTP +
Sbjct: 715 NHEVMMRGTFANVRIKNLMIPPRDDGSREEGGLTLFQPSGEKMFIYDAAMKYIAEGTPTV 774

Query: 771 VIAGKEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETL 830
           +  G+EYGTGSSRDWAAKGT LLGI+AV+A SFERIHRSNLVGMGVLPL+F+  ++ ++L
Sbjct: 775 IFGGEEYGTGSSRDWAAKGTQLLGIKAVVARSFERIHRSNLVGMGVLPLQFIGDDSWQSL 834

Query: 831 GLTGYEVYDILGLEDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTV 890
           GL G E+ DI   E L+P+    ++  + DGS    +   R+DTP+EVDYY++GGIL  V
Sbjct: 835 GLRGDELIDIETDEALRPQSEARLIITKPDGSRTETRLRLRIDTPIEVDYYRHGGILPFV 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: 2248
Number of extensions: 122
Number of successful extensions: 10
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 24 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
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