Alignments for a candidate for acn in Ochrobactrum thiophenivorans DSM 7216

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Ochrobactrum thiophenivorans DSM 7216

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_094506127.1 CEV31_RS06075 aconitate hydratase AcnA

Query= SwissProt::P70920
         (906 letters)



>NCBI__GCF_002252445.1:WP_094506127.1
          Length = 895

 Score = 1299 bits (3362), Expect = 0.0
 Identities = 650/907 (71%), Positives = 750/907 (82%), Gaps = 13/907 (1%)

Query: 1   MTSLDSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVK 60
           M+ +DSFKC+KTL VG K YVYYSL  AEKNGL G+SKLP+SMKVLLENLLR ED R+VK
Sbjct: 1   MSHIDSFKCRKTLTVGGKEYVYYSLTEAEKNGLTGVSKLPFSMKVLLENLLRFEDDRTVK 60

Query: 61  KADIVAVSKWLRKK-SLEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKIN 119
           K+DI A++ WL  + S   EIA+RPARVLMQDFTGVPAVVDLAAMR+ ++ LGGD EKIN
Sbjct: 61  KSDIEAIAAWLNDRGSAGAEIAYRPARVLMQDFTGVPAVVDLAAMRDGLKALGGDPEKIN 120

Query: 120 PLVPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTG 179
           PLVPVDLVIDHSVIV+ FG+  AF  NV  EY++N ERY FLKWGQ AF NF VVPPGTG
Sbjct: 121 PLVPVDLVIDHSVIVDEFGNPSAFKANVDLEYQRNGERYRFLKWGQQAFKNFRVVPPGTG 180

Query: 180 ICHQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGG 239
           ICHQVNLEYL+Q VWTK+E            VAYPD+ VGTDSHTTMVNGL VLGWGVGG
Sbjct: 181 ICHQVNLEYLAQAVWTKEEDGET--------VAYPDTCVGTDSHTTMVNGLGVLGWGVGG 232

Query: 240 IEAEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGP 299
           IEAEA MLGQP+SMLLP V+GF+L G +KEGVTATDLVLTVTQMLRK GVVGKFVEFFG 
Sbjct: 233 IEAEAAMLGQPVSMLLPEVIGFRLTGKVKEGVTATDLVLTVTQMLRKKGVVGKFVEFFGE 292

Query: 300 GLDHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLF 359
           GLD++++AD+ATIANM PEYGATCGFFP+D   ++Y+ T+GRA  R+ALV+AY++AQG++
Sbjct: 293 GLDNMTLADRATIANMGPEYGATCGFFPIDNETLNYMNTTGRAEDRMALVEAYSRAQGMW 352

Query: 360 RTAKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAK 419
           R A S DPVFT+ L LD+++VVPSMAGPKRPEGRIAL ++  GF+ +L  EYKKT   A 
Sbjct: 353 REAGSEDPVFTDILELDMSEVVPSMAGPKRPEGRIALENIGSGFATSLETEYKKTTGQAA 412

Query: 420 RFAVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAP 479
           R+AVEG+ +++GHGDV IAAITSCTNTSNPSVLI AGLLARNA AKGLK KPWVKTSLAP
Sbjct: 413 RYAVEGEDFDLGHGDVAIAAITSCTNTSNPSVLIAAGLLARNAVAKGLKTKPWVKTSLAP 472

Query: 480 GSQVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLS 539
           GSQVVAAYL  +GLQ  LD +GFNLVGFGCTTCIGNSGPLP  ISK+IN+ G++AAAVLS
Sbjct: 473 GSQVVAAYLESAGLQKDLDALGFNLVGFGCTTCIGNSGPLPAPISKTINEKGLIAAAVLS 532

Query: 540 GNRNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTS 599
           GNRNFEGRVSPDVQANYLASPPLVVAHALAG+VTK+L  EPLGE ++G PV+L+DIWP+S
Sbjct: 533 GNRNFEGRVSPDVQANYLASPPLVVAHALAGTVTKDLTKEPLGEDQNGNPVFLRDIWPSS 592

Query: 600 KEINAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMK 659
            EI  F+ K VT  IF +KYADVFKGD NW+ ++    +TY W+ +STYVQNPPYF GM 
Sbjct: 593 AEIQEFIAKNVTRKIFSEKYADVFKGDENWQAVQVPAGQTYAWDDNSTYVQNPPYFVGMG 652

Query: 660 KEPEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRR 719
           K    + D+  AR+L +FGDKITTDHISPAGSIK  SPAGKYL +H V  ADFNQYGTRR
Sbjct: 653 KSAGTIADVKGARVLGLFGDKITTDHISPAGSIKAQSPAGKYLIDHGVGIADFNQYGTRR 712

Query: 720 GNHEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLV 779
           GNHEVMMRGTFANIRI+N ML G +G   EGG T H+P  E+ SIYDAAM+Y+ E VPLV
Sbjct: 713 GNHEVMMRGTFANIRIRNHML-GENGR--EGGYTIHYPSKEETSIYDAAMQYKAEGVPLV 769

Query: 780 VFAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSL 839
           VFAG EYGNGSSRDWAAKGT LLGV+AVI QSFERIHRSNLVGMG++P  FEEGTSW +L
Sbjct: 770 VFAGVEYGNGSSRDWAAKGTNLLGVKAVIAQSFERIHRSNLVGMGIVPFVFEEGTSWQTL 829

Query: 840 GLKGDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHY 899
           GLKGDE V++ GL  D++PRQK+ A I   DGS+++V L+CRIDTLDELDY +NGGIL  
Sbjct: 830 GLKGDEIVSIEGL-ADVRPRQKIEASITFADGSVKKVPLICRIDTLDELDYMKNGGILQT 888

Query: 900 VLRKLAA 906
           VLR LAA
Sbjct: 889 VLRDLAA 895


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: 2239
Number of extensions: 92
Number of successful extensions: 5
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: 895
Length adjustment: 43
Effective length of query: 863
Effective length of database: 852
Effective search space:   735276
Effective search space used:   735276
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