GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_06606
          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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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