Alignments for a candidate for acn in Rhodopseudomonas pseudopalustris DSM 123

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Rhodopseudomonas pseudopalustris DSM 123

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_092685791.1 BMY71_RS19130 aconitate hydratase AcnA

Query= SwissProt::P70920
         (906 letters)



>NCBI__GCF_900110435.1:WP_092685791.1
          Length = 905

 Score = 1647 bits (4264), Expect = 0.0
 Identities = 811/906 (89%), Positives = 867/906 (95%), Gaps = 1/906 (0%)

Query: 1   MTSLDSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVK 60
           MTSLDSFKC+K LKVG+K+YVYYSLPTAEKNGLKGIS+LPYSMKVLLENLLRNED R+VK
Sbjct: 1   MTSLDSFKCRKILKVGSKSYVYYSLPTAEKNGLKGISRLPYSMKVLLENLLRNEDDRTVK 60

Query: 61  KADIVAVSKWLRKKSLEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINP 120
           KADI AV+KW+RKK+LEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQ LGGDAEKINP
Sbjct: 61  KADIQAVAKWMRKKALEHEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQALGGDAEKINP 120

Query: 121 LVPVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGI 180
           LVPVDLVIDHSVIVNFFGDNKAF KNV EEYKQNQERYEFLKWGQ AFSNF+VVPPGTGI
Sbjct: 121 LVPVDLVIDHSVIVNFFGDNKAFGKNVAEEYKQNQERYEFLKWGQKAFSNFAVVPPGTGI 180

Query: 181 CHQVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGI 240
           CHQVNLEYL+QTVWT+KEKMT+GKK GTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGI
Sbjct: 181 CHQVNLEYLAQTVWTRKEKMTIGKKKGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGI 240

Query: 241 EAEACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPG 300
           EAEA MLGQPLSMLLP VVGFKLKGA+KEGVTATDLVLTVTQMLRK GVVGKFVEFFGPG
Sbjct: 241 EAEAAMLGQPLSMLLPEVVGFKLKGALKEGVTATDLVLTVTQMLRKQGVVGKFVEFFGPG 300

Query: 301 LDHLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFR 360
           LDHLSVADK+TIANMAPEYGATCGFFPVD   +DYLKTSGRA+ RVALV+ YAKAQGLFR
Sbjct: 301 LDHLSVADKSTIANMAPEYGATCGFFPVDTETLDYLKTSGRASARVALVEKYAKAQGLFR 360

Query: 361 TAKSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAKR 420
           TAKSADPVFT TLTLDLA VVPS+AGPKRPEGR+ALP+V+EGF+ A+  EYKK  + A R
Sbjct: 361 TAKSADPVFTVTLTLDLASVVPSLAGPKRPEGRVALPTVSEGFTAAMDAEYKKALDGA-R 419

Query: 421 FAVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAPG 480
           +AV+G+K+++GHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKA PWVKTSLAPG
Sbjct: 420 YAVDGRKFDLGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAAPWVKTSLAPG 479

Query: 481 SQVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLSG 540
           SQVVA YLA+SGLQ  LDKVGFNLVGFGCTTCIGNSGPLPE+ISKSINDNGIVAAAVLSG
Sbjct: 480 SQVVAEYLANSGLQKDLDKVGFNLVGFGCTTCIGNSGPLPEDISKSINDNGIVAAAVLSG 539

Query: 541 NRNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTSK 600
           NRNFEGRVSPDVQANYLASPPLVVA+ALAG+VTKNLAVEP+G GKDGKPVYLKDIWPT+K
Sbjct: 540 NRNFEGRVSPDVQANYLASPPLVVAYALAGTVTKNLAVEPIGTGKDGKPVYLKDIWPTTK 599

Query: 601 EINAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMKK 660
           EINAF+KK+VTA+IFKKKYADVFKGDTNWRKIKTV+SETY+WNMSSTYVQNPPYFEGMK 
Sbjct: 600 EINAFVKKYVTAAIFKKKYADVFKGDTNWRKIKTVDSETYKWNMSSTYVQNPPYFEGMKM 659

Query: 661 EPEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRG 720
           +PEP+ D+V+ARILA+FGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRG
Sbjct: 660 QPEPIVDVVDARILAVFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRG 719

Query: 721 NHEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLVV 780
           NHEVMMRGTFANIRIKN MLKGADGNIPEGGLTKHWPDG+QMSIYDAAMKYQ EQVPLVV
Sbjct: 720 NHEVMMRGTFANIRIKNHMLKGADGNIPEGGLTKHWPDGDQMSIYDAAMKYQAEQVPLVV 779

Query: 781 FAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSLG 840
           FAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFE+GTSW+SLG
Sbjct: 780 FAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEDGTSWASLG 839

Query: 841 LKGDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHYV 900
           +KGDEKVT+RGL GDLKPRQ LTAEI +G+G ++RV LLCRIDTLDEL+YYRNGGILHYV
Sbjct: 840 IKGDEKVTIRGLQGDLKPRQTLTAEIKAGNGKVKRVPLLCRIDTLDELEYYRNGGILHYV 899

Query: 901 LRKLAA 906
           LRKLAA
Sbjct: 900 LRKLAA 905


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: 2511
Number of extensions: 90
Number of successful extensions: 2
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 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