Alignments for a candidate for acn in Hyphomicrobium sulfonivorans WDL6

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Hyphomicrobium sulfonivorans WDL6

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_068459766.1 APY04_RS03620 aconitate hydratase AcnA

Query= SwissProt::P70920
         (906 letters)



>NCBI__GCF_001541235.1:WP_068459766.1
          Length = 905

 Score = 1348 bits (3490), Expect = 0.0
 Identities = 667/905 (73%), Positives = 766/905 (84%), Gaps = 9/905 (0%)

Query: 3   SLDSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVKKA 62
           SLDSFKC++T+  G KTY YYSLP AEKNGL GIS+LP+SM+VLLENLLR+EDGR+V K 
Sbjct: 8   SLDSFKCRRTISAGGKTYTYYSLPEAEKNGLAGISRLPFSMRVLLENLLRHEDGRTVTKT 67

Query: 63  DIVAVSKWLRKKSLE-HEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPL 121
           DI AV+ WL  K     EI FRPARVLMQDFTGVPAVVDLAAMR+ M+ LGGDA+KINPL
Sbjct: 68  DIEAVAAWLNDKGKAGKEIGFRPARVLMQDFTGVPAVVDLAAMRDGMKSLGGDAQKINPL 127

Query: 122 VPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGIC 181
           VPVDLVIDHSVIV+ FG  +AFA+NV  EYK+N ERY FLKWGQ AF NF VVPPGTGIC
Sbjct: 128 VPVDLVIDHSVIVDEFGSPQAFAQNVELEYKRNVERYNFLKWGQGAFDNFRVVPPGTGIC 187

Query: 182 HQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIE 241
           HQVNLE+L+QTVWT++         GT  +AYPD+LVGTDSHTTMVNGLAVLGWGVGGIE
Sbjct: 188 HQVNLEFLAQTVWTRE------LPDGTI-LAYPDTLVGTDSHTTMVNGLAVLGWGVGGIE 240

Query: 242 AEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGL 301
           AEA MLGQ  SMLLP V+GFKL G + EGVTATDLVLTVTQMLRK GVVGKFVEF+GPGL
Sbjct: 241 AEAAMLGQAQSMLLPEVIGFKLTGKVNEGVTATDLVLTVTQMLRKKGVVGKFVEFYGPGL 300

Query: 302 DHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRT 361
           D + +AD+ATIANMAPEYGATCGFFP+D   ++YL+ SGR + R+ LV+ YAKAQ ++R 
Sbjct: 301 DTMPLADRATIANMAPEYGATCGFFPIDGETLNYLRISGRESGRIELVEEYAKAQNMYRI 360

Query: 362 AKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAKRF 421
           A S DPVFT+TL LDL+ VVPSMAGPKRPEGRIALP VA GF+ ALA EYKKT + + RF
Sbjct: 361 AGSEDPVFTDTLELDLSTVVPSMAGPKRPEGRIALPDVAPGFATALAGEYKKTGDTSARF 420

Query: 422 AVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAPGS 481
            V+G+ ++IGHGDVVI AITSCTNTSNPSVLI AGLLA+ A  KGL AKPWVKTSLAPGS
Sbjct: 421 PVKGRDFDIGHGDVVITAITSCTNTSNPSVLIAAGLLAKKAVEKGLTAKPWVKTSLAPGS 480

Query: 482 QVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLSGN 541
           QVV+AYL  +GLQ +LDKVGFNLVGFGCTTCIGNSGPL  EIS +IN+NGIVAAAVLSGN
Sbjct: 481 QVVSAYLEKAGLQPYLDKVGFNLVGFGCTTCIGNSGPLAPEISATINENGIVAAAVLSGN 540

Query: 542 RNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTSKE 601
           RNFEGRVSPDVQANYLASPPLVVA+ALAG+V K+L VEP+G G DG+PVYL+DIWP+S+E
Sbjct: 541 RNFEGRVSPDVQANYLASPPLVVAYALAGTVAKDLTVEPIGIGSDGEPVYLRDIWPSSQE 600

Query: 602 INAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMKKE 661
           I+ F+ + +T  +F ++YADVF GD +WR I T   ETY W+  STYV+NPPYFEG+ K+
Sbjct: 601 IHRFIAENITRELFLERYADVFNGDASWRAIDTAGGETYTWDDDSTYVRNPPYFEGISKD 660

Query: 662 PEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRGN 721
           P P++DI  ARIL +FGDKITTDHISPAGSIK +SPAG+YLS H V  ADFNQYGTRRGN
Sbjct: 661 PRPISDIKGARILGLFGDKITTDHISPAGSIKPSSPAGEYLSSHDVAVADFNQYGTRRGN 720

Query: 722 HEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLVVF 781
           HEVMMRGTFANIRIKNFML+ ADGN+ EGG T H+P G+QMSIYDAAM+Y+ E VPLVVF
Sbjct: 721 HEVMMRGTFANIRIKNFMLRDADGNVKEGGNTVHYPSGQQMSIYDAAMRYRDENVPLVVF 780

Query: 782 AGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSLGL 841
           AG EYGNGSSRDWAAKGT LLGVRAVI QSFERIHRSNLVGMG++P  FEEGTSW +LGL
Sbjct: 781 AGVEYGNGSSRDWAAKGTNLLGVRAVISQSFERIHRSNLVGMGIVPFVFEEGTSWETLGL 840

Query: 842 KGDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHYVL 901
           KGDE V++ GL   +KPRQK+ AEI S DG++++V ++CRIDTLDE++Y+RNGGILHYVL
Sbjct: 841 KGDEIVSIPGLT-TIKPRQKMEAEITSADGTVRKVPIICRIDTLDEIEYFRNGGILHYVL 899

Query: 902 RKLAA 906
           R LAA
Sbjct: 900 RNLAA 904


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: 2332
Number of extensions: 87
Number of successful extensions: 4
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: 905
Length adjustment: 43
Effective length of query: 863
Effective length of database: 862
Effective search space:   743906
Effective search space used:   743906
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
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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 2024 update 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