Alignments for a candidate for acnD in Thiohalospira halophila HL 3

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Thiohalospira halophila HL 3

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_093427176.1 BM272_RS02610 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_900112605.1:WP_093427176.1
          Length = 914

 Score =  711 bits (1834), Expect = 0.0
 Identities = 392/909 (43%), Positives = 541/909 (59%), Gaps = 79/909 (8%)

Query: 19  DYFDTREAIEA-----------IAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQII- 66
           D F  R  +EA             PG+  +LPY+ ++L ENL+R  +   +TA   Q + 
Sbjct: 3   DSFQARAELEAGGNRYRYVRLDAVPGS-ERLPYSLKILLENLLRHEDGRTVTAEDIQRLA 61

Query: 67  ----ESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIV 122
               +++   +  + PARV+  D  G  A+VDLA +RDA+A  GGDP  +NP+ P +L++
Sbjct: 62  NWDPQAEPAHEIAFRPARVLMQDFTGVPAVVDLAAMRDAMAELGGDPEHINPLQPAELVI 121

Query: 123 DHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLE 182
           DHS+ V++ G + +A+  N A+E +RN +R+ F+ W Q +F N   +P G GI+HQINLE
Sbjct: 122 DHSVQVDHYG-NGEAYGLNEALEYQRNRERYTFLKWGQGSFANFKAVPPGKGIVHQINLE 180

Query: 183 RMSPVIHARNGV-----AFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMR 237
            +  V+    G      A+PDTLVGTDSHTP ++ LGV+  GVGG+EAE+ MLG+   M 
Sbjct: 181 HLGRVVFGAEGPDGAQWAWPDTLVGTDSHTPMINGLGVLGWGVGGIEAEAAMLGQPISML 240

Query: 238 LPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISN 297
           +P ++G  LTG+   G TATD+VL + E LRA  VV  ++EFFG+G + L + DRATI+N
Sbjct: 241 VPQVVGFRLTGQLPEGATATDLVLTIVEQLRAHGVVGKFVEFFGDGLDELPIADRATIAN 300

Query: 298 MTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDD-LKQAVYPRTLH 356
           M PE+GAT  +F +D  TLDYL LTGR  +QV  VE YA+  GL+ +    +A Y   + 
Sbjct: 301 MAPEYGATCGIFPVDTATLDYLRLTGRSEDQVARVEAYARAQGLFRESGAPEAAYTSVVE 360

Query: 357 FDLSSVVRTIAGPSNPHARVPTSE------------LAARGISGEVENE----------- 393
            DL+++  ++AGP  P  R+  S+            L+ RG+    + E           
Sbjct: 361 LDLATIEPSLAGPRRPQDRIALSQARRPIRESLDGILSERGMVPREDRETERFAAEGGHT 420

Query: 394 -PGL--------------------MPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAK 432
            PG+                    + DG V+IAAITSCTNTSNP  ++ AGLLA+ A  +
Sbjct: 421 APGVEHQGDHRGKVRVERNGESFYLDDGMVVIAAITSCTNTSNPSVMLGAGLLAKKALER 480

Query: 433 GLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQ 492
           GL  KPWVKTSL PGS+ V  YLE A LL +LE LGF +VG+ CTTC G SG LD  I  
Sbjct: 481 GLQVKPWVKTSLGPGSRVVTDYLEHAGLLDDLEGLGFDVVGYGCTTCIGNSGPLDESISH 540

Query: 493 EVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDK 552
            + + DL   ++LSGNRNF+GRIH   +  +LASPPLVVAYA+AG +  D   D LG D 
Sbjct: 541 AIREDDLVVCSILSGNRNFEGRIHSEVRMNYLASPPLVVAYALAGRMDIDPYNDALGTDA 600

Query: 553 DGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQ 609
           DG  V L +IWPS AEI A++   V+ + F + Y  +F     +    +P   LYDW   
Sbjct: 601 DGNAVYLRDIWPSQAEIQALVRDHVRADAFEQAYADVFAGGERWEALTAPGGRLYDWAED 660

Query: 610 STYIRRPPYWEGALAGER---TLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKM 666
           STYIRRPP++EG          + G R LAV+GD++TTDH+SP+ +I  DS AG YL + 
Sbjct: 661 STYIRRPPFFEGIQPEPEPVGDITGARALAVVGDSVTTDHISPAGSIAADSPAGHYLREN 720

Query: 667 GLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWE 726
           G+   +FNSY   RG+H    R TFANP+ +N +A       +G     +P G V  +++
Sbjct: 721 GVEPAEFNSYGARRGNHEVMMRGTFANPRFRNRLA----PDTEGGWTAHQPSGKVMPIYD 776

Query: 727 AIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVL 786
           A   Y +   PL+++AG +YG GSSRDWAAKG RL GV A++AE +ERIHR+NLVGMG+L
Sbjct: 777 AAMRYAEEGTPLVVLAGKEYGSGSSRDWAAKGPRLLGVRAVIAESYERIHRSNLVGMGIL 836

Query: 787 PLEFKAGENRATYGIDGTEVFDVIGSIAPRAD-LTVIITRKNGERVEVPVTCRLDTAEEV 845
           PL+F+ G+   + G+DGTE F + G     AD +TV  T  +G         R+DT +EV
Sbjct: 837 PLQFRDGDTADSLGLDGTETFALAGLGDGSADQVTVTATTADGGETTFTARVRIDTPQEV 896

Query: 846 SIYEAGGVL 854
             Y  GG+L
Sbjct: 897 EYYRHGGIL 905


Lambda     K      H
   0.318    0.136    0.397 

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: 2168
Number of extensions: 103
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 867
Length of database: 914
Length adjustment: 43
Effective length of query: 824
Effective length of database: 871
Effective search space:   717704
Effective search space used:   717704
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 (21.7 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