Aligments for a candidate for acn in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for acn in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_06606 H281DRAFT_06606 aconitase

Query= SwissProt::Q5SMF6
         (902 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06606 H281DRAFT_06606
           aconitase
          Length = 905

 Score =  965 bits (2495), Expect = 0.0
 Identities = 495/905 (54%), Positives = 638/905 (70%), Gaps = 17/905 (1%)

Query: 3   NSFQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDI 62
           N  +TLK   + SG   +Y L +L +    ++ RLP SIR++LES+LRN DG ++  E I
Sbjct: 4   NLHKTLKEFDSGSGKGKFYSLPQLGKALNIKIDRLPVSIRIVLESVLRNYDGKKIAEEHI 63

Query: 63  EALARWRPDPGEIN-VPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPA 121
             LA W+P    ++ +P  ++RV+LQDFTGVP + D+AAMR   +  G +PK I P+VP 
Sbjct: 64  TQLANWKPTAPRVDEIPFVVSRVVLQDFTGVPLLADIAAMRGVAQRVGKNPKSIEPLVPV 123

Query: 122 DLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQV 181
           DLV+DHSVQ+D F    A   N++ E++RN ERY  +KW   A + F+VVPPG GIVHQV
Sbjct: 124 DLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQFMKWGMQAFDTFKVVPPGVGIVHQV 183

Query: 182 NIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYY 241
           N+EYL + V        T+ +PDSLVGTDSHTTM+NG+GV+GWGVGGIEAEA MLGQP Y
Sbjct: 184 NLEYLARGVHKKAEGADTVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPVY 243

Query: 242 MLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATI 301
            L P VVG  L G+L EG TATDLVLT+TE+LRK  VVGKFVEF+G G   LS PDRATI
Sbjct: 244 FLTPDVVGVNLKGKLREGVTATDLVLTITELLRKEKVVGKFVEFFGEGTRSLSLPDRATI 303

Query: 302 ANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSE 361
            NMAPEYGATMGFFPVDE+T++Y + TGR +  +   + Y KA  LF  P+ E  + +++
Sbjct: 304 GNMAPEYGATMGFFPVDEKTIDYFKGTGRTDAEISAFQNYFKAQNLFGIPK-EGDIDFTK 362

Query: 362 YLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVKR 421
            + LDL  V PSLAGPKRPQDR+ +  VK +F    +KPV E GF   E  L  +     
Sbjct: 363 VVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFSKPVAENGFAKKEADLDAQYTT-- 420

Query: 422 RDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSKV 481
                 + +G V+IAAITSCTNTSNPSV+L AGLLAKKAVEAGL   P +KTSLAPGS++
Sbjct: 421 -SNGVNVKNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRI 479

Query: 482 VTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNRN 541
           VT+YL  +GL+P+L+ LGF L  YGCTTCIGN+G L  ++ +A+ + ++V AAVLSGNRN
Sbjct: 480 VTEYLTKTGLLPYLDKLGFTLAAYGCTTCIGNAGDLTPELNEAITKNDIVAAAVLSGNRN 539

Query: 542 FEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEIR 601
           FE RI+P+++AN+LASP LVVAYA+AG +  D  TEP+G    GK +YL DIWP+ +E+ 
Sbjct: 540 FEARIHPNIRANFLASPPLVVAYAIAGNITRDLMTEPVGKGKGGKDVYLGDIWPTSDEVN 599

Query: 602 EAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFF-EDLGERK 660
           + ++  LD + F+K Y+ + +  + W  +    G++Y W P+STYI  PPFF  D     
Sbjct: 600 DLLKFALDADAFRKNYASLTKKGDLWSKIEGEEGQVYDW-PKSTYIAEPPFFGNDFSMTP 658

Query: 661 VEDI---RGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGN 717
            + I   + AR L + GDSVTTDHISPAG+I   SPAG++L   GV+  DFNSYGSRRGN
Sbjct: 659 ADSIAAVKNARALGIFGDSVTTDHISPAGSIKEDSPAGKWLKENGVQKADFNSYGSRRGN 718

Query: 718 HEVMMRGTFANIRIKNLML----DG--IEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLV 771
           H+VMMRGTFAN+RIKNLM+    DG  +EGG     P G+   +Y+ AM+Y   GTP +V
Sbjct: 719 HDVMMRGTFANVRIKNLMIPAKADGSRVEGGLTIHQPSGEQLSIYDAAMKYIDAGTPTIV 778

Query: 772 IAGKEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLG 831
            AG+EYGTGSSRDWAAKGT LLG++AV+A SFERIHRSNLVGMGVLPL+F   ++ ++LG
Sbjct: 779 FAGEEYGTGSSRDWAAKGTQLLGVKAVVARSFERIHRSNLVGMGVLPLQFKGSDSVQSLG 838

Query: 832 LTGYEVYDILGL-EDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTV 890
           +TG E YDI GL  D KP++ V +V R +DGSE R   + R+DTP+EVDYYK+GGIL  V
Sbjct: 839 ITGEETYDIEGLGADFKPQQEVTLVIRGKDGSEKRVPVLLRIDTPIEVDYYKHGGILPFV 898

Query: 891 LLNML 895
           L ++L
Sbjct: 899 LRSLL 903


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: 2197
Number of extensions: 106
Number of successful extensions: 8
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: 905
Length adjustment: 43
Effective length of query: 859
Effective length of database: 862
Effective search space:   740458
Effective search space used:   740458
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