GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Sinorhizobium meliloti 1021

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 SMc03846 SMc03846 aconitate hydratase

Query= SwissProt::P70920
         (906 letters)



>FitnessBrowser__Smeli:SMc03846
          Length = 896

 Score = 1298 bits (3359), Expect = 0.0
 Identities = 652/905 (72%), Positives = 742/905 (81%), Gaps = 13/905 (1%)

Query: 3   SLDSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVKKA 62
           SLDSF C+ TL V    YVYYSLP AE NGL GISKLPYSMKVLLENLLRNEDGRSV K 
Sbjct: 4   SLDSFNCRSTLTVNGVDYVYYSLPKAEANGLAGISKLPYSMKVLLENLLRNEDGRSVTKK 63

Query: 63  DIVAVSKWLRKK-SLEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPL 121
           DI  ++ WL  K + E+EIA+RPARVLMQDFTGVPAVVDLAAMR+AM  LGGD EKINPL
Sbjct: 64  DIENIAAWLGDKGTAENEIAYRPARVLMQDFTGVPAVVDLAAMRDAMVSLGGDPEKINPL 123

Query: 122 VPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGIC 181
           VPVDLVIDHSVIV+ FG   AFA+NV  EY++N ERY FLKWGQ AF NF VVPPGTGIC
Sbjct: 124 VPVDLVIDHSVIVDEFGTPTAFARNVELEYQRNGERYRFLKWGQQAFKNFRVVPPGTGIC 183

Query: 182 HQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIE 241
           HQVNLEYL Q VWT++E   V         AYPD+ VGTDSHTTM+NGL VLGWGVGGIE
Sbjct: 184 HQVNLEYLGQAVWTREEDGEV--------TAYPDTCVGTDSHTTMINGLGVLGWGVGGIE 235

Query: 242 AEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGL 301
           AEA MLGQP+SMLLP V+GFKL G +KEGVTATDLVLTV QMLRK GVV KFVEFFGPGL
Sbjct: 236 AEAAMLGQPVSMLLPEVIGFKLTGKLKEGVTATDLVLTVVQMLRKKGVVSKFVEFFGPGL 295

Query: 302 DHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRT 361
           D++++AD+ATI NM PEYGATCGFFPVDA  I+YL  SGR   R+ALV+AY+KAQG++R 
Sbjct: 296 DNMTLADRATIGNMGPEYGATCGFFPVDAETINYLTISGREEQRIALVEAYSKAQGMWRE 355

Query: 362 AKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAKRF 421
              ++ VFT+TL LDL DVVPSMAGPKRPEGRIAL ++A GF+ AL N+YKK  + A R+
Sbjct: 356 GDGSELVFTDTLELDLGDVVPSMAGPKRPEGRIALENIASGFAAALDNDYKKPGQLANRY 415

Query: 422 AVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAPGS 481
           AVEG  Y++GHGDV IAAITSCTNTSNPSVLI AGLLARNA AKGLK +PWVKTSLAPGS
Sbjct: 416 AVEGTDYDLGHGDVAIAAITSCTNTSNPSVLIAAGLLARNAVAKGLKTQPWVKTSLAPGS 475

Query: 482 QVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLSGN 541
           QVVA YL+ SGLQ  LDK+GFNLVGFGCTTCIGNSGPLP EISK+IND G++AA VLSGN
Sbjct: 476 QVVAEYLSKSGLQTDLDKLGFNLVGFGCTTCIGNSGPLPTEISKTINDKGLIAAGVLSGN 535

Query: 542 RNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTSKE 601
           RNFEGR+SPDVQANYLASPPLVVA+ALAGSV K+L  EP+GE +DG+PVYL+DIWPTS+E
Sbjct: 536 RNFEGRISPDVQANYLASPPLVVAYALAGSVQKDLTKEPIGEDRDGQPVYLRDIWPTSQE 595

Query: 602 INAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMKKE 661
           I  F+ ++VT  ++  KYADVFKGD NW+ ++    +TY W+  STYVQNPPYF GM K+
Sbjct: 596 IQDFIFRYVTRELYATKYADVFKGDANWQAVQVPAGQTYAWDEGSTYVQNPPYFVGMGKK 655

Query: 662 PEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRGN 721
              ++DI  AR+L +FGDKITTDHISPAGSIK  SPAG YL EH V  ADFNQYGTRRGN
Sbjct: 656 GAGISDIKNARVLGLFGDKITTDHISPAGSIKAASPAGAYLLEHGVGIADFNQYGTRRGN 715

Query: 722 HEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLVVF 781
           HEVMMRGTFANIRI+N ML G +G   EGG T H+P  E+MSIYDAAM+Y++E VPLV+F
Sbjct: 716 HEVMMRGTFANIRIRNHML-GPNGK--EGGYTIHYPSKEEMSIYDAAMQYKEEGVPLVIF 772

Query: 782 AGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSLGL 841
           AG EYGNGSSRDWAAKGT LLGV+AVI QSFERIHRSNLVGMGV+P  FEEG +W SLGL
Sbjct: 773 AGVEYGNGSSRDWAAKGTNLLGVKAVIAQSFERIHRSNLVGMGVVPFVFEEGMTWESLGL 832

Query: 842 KGDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHYVL 901
           KGDE VT+  L  +++PR+K  A+I  GDGS++ V L+CRIDTLDE+ Y  NGGIL  VL
Sbjct: 833 KGDEVVTIENL-ANVQPREKRVAKITYGDGSVKEVPLICRIDTLDEVTYVNNGGILQTVL 891

Query: 902 RKLAA 906
           R LAA
Sbjct: 892 RDLAA 896


Lambda     K      H
   0.317    0.134    0.393 

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: 2261
Number of extensions: 88
Number of successful extensions: 6
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: 906
Length of database: 896
Length adjustment: 43
Effective length of query: 863
Effective length of database: 853
Effective search space:   736139
Effective search space used:   736139
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