Alignments for a candidate for acnD in Hyphomicrobium sulfonivorans WDL6

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Hyphomicrobium sulfonivorans WDL6

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_068459766.1 APY04_RS03620 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_001541235.1:WP_068459766.1
          Length = 905

 Score =  709 bits (1830), Expect = 0.0
 Identities = 389/878 (44%), Positives = 539/878 (61%), Gaps = 42/878 (4%)

Query: 15  GTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVR--------RCEPEMLTASLKQII 66
           G    Y+   EA E       ++LP++ RVL ENL+R        + + E + A L    
Sbjct: 22  GKTYTYYSLPEA-EKNGLAGISRLPFSMRVLLENLLRHEDGRTVTKTDIEAVAAWLNDKG 80

Query: 67  ESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSL 126
           ++ +E+ F   PARV+  D  G  A+VDLA +RD + + GGD  ++NP+VP  L++DHS+
Sbjct: 81  KAGKEIGFR--PARVLMQDFTGVPAVVDLAAMRDGMKSLGGDAQKINPLVPVDLVIDHSV 138

Query: 127 AVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSP 186
            V+  G    AFA+N  +E +RN +R++F+ W Q AF N  V+P G GI HQ+NLE ++ 
Sbjct: 139 IVDEFG-SPQAFAQNVELEYKRNVERYNFLKWGQGAFDNFRVVPPGTGICHQVNLEFLAQ 197

Query: 187 VIHARNG-----VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDI 241
            +  R       +A+PDTLVGTDSHT  V+ L V+  GVGG+EAE+ MLG+A  M LP++
Sbjct: 198 TVWTRELPDGTILAYPDTLVGTDSHTTMVNGLAVLGWGVGGIEAEAAMLGQAQSMLLPEV 257

Query: 242 IGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPE 301
           IG +LTGK   G+TATD+VL +T+ LR + VV  ++EF+G G + + L DRATI+NM PE
Sbjct: 258 IGFKLTGKVNEGVTATDLVLTVTQMLRKKGVVGKFVEFYGPGLDTMPLADRATIANMAPE 317

Query: 302 FGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWS-DDLKQAVYPRTLHFDLS 360
           +GAT   F ID +TL+YL ++GRE+ +++LVE YAK   ++     +  V+  TL  DLS
Sbjct: 318 YGATCGFFPIDGETLNYLRISGRESGRIELVEEYAKAQNMYRIAGSEDPVFTDTLELDLS 377

Query: 361 SVVRTIAGPSNPHARVPTSELA---ARGISGE------------VENEPGLMPDGAVIIA 405
           +VV ++AGP  P  R+   ++A   A  ++GE            V+     +  G V+I 
Sbjct: 378 TVVPSMAGPKRPEGRIALPDVAPGFATALAGEYKKTGDTSARFPVKGRDFDIGHGDVVIT 437

Query: 406 AITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELE 465
           AITSCTNTSNP  +IAAGLLA+ A  KGLT KPWVKTSLAPGS+ V  YLE+A L P L+
Sbjct: 438 AITSCTNTSNPSVLIAAGLLAKKAVEKGLTAKPWVKTSLAPGSQVVSAYLEKAGLQPYLD 497

Query: 466 SLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLA 525
            +GF +VGF CTTC G SG L P I   + +  + A AVLSGNRNF+GR+ P  +  +LA
Sbjct: 498 KVGFNLVGFGCTTCIGNSGPLAPEISATINENGIVAAAVLSGNRNFEGRVSPDVQANYLA 557

Query: 526 SPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKV 585
           SPPLVVAYA+AGT+  D+  + +G+  DG+PV L +IWPS  EI   IA ++  E F + 
Sbjct: 558 SPPLVVAYALAGTVAKDLTVEPIGIGSDGEPVYLRDIWPSSQEIHRFIAENITRELFLER 617

Query: 586 YEPMFDLSVDY---GDKVSPLYDWRPQSTYIRRPPYWEGALAGER---TLKGMRPLAVLG 639
           Y  +F+    +          Y W   STY+R PPY+EG     R    +KG R L + G
Sbjct: 618 YADVFNGDASWRAIDTAGGETYTWDDDSTYVRNPPYFEGISKDPRPISDIKGARILGLFG 677

Query: 640 DNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNE 699
           D ITTDH+SP+ +I   S AGEYL    +   DFN Y T RG+H    R TFAN ++KN 
Sbjct: 678 DKITTDHISPAGSIKPSSPAGEYLSSHDVAVADFNQYGTRRGNHEVMMRGTFANIRIKNF 737

Query: 700 M-AIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKG 758
           M    DG VK+G      P G    +++A   Y D   PL++ AG +YG GSSRDWAAKG
Sbjct: 738 MLRDADGNVKEGGNTVHYPSGQQMSIYDAAMRYRDENVPLVVFAGVEYGNGSSRDWAAKG 797

Query: 759 VRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG--SIAPR 816
             L GV A++++ FERIHR+NLVGMG++P  F+ G +  T G+ G E+  + G  +I PR
Sbjct: 798 TNLLGVRAVISQSFERIHRSNLVGMGIVPFVFEEGTSWETLGLKGDEIVSIPGLTTIKPR 857

Query: 817 ADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854
             +   IT  +G   +VP+ CR+DT +E+  +  GG+L
Sbjct: 858 QKMEAEITSADGTVRKVPIICRIDTLDEIEYFRNGGIL 895


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: 2072
Number of extensions: 117
Number of successful extensions: 11
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: 867
Length of database: 905
Length adjustment: 43
Effective length of query: 824
Effective length of database: 862
Effective search space:   710288
Effective search space used:   710288
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 Apr 09 2024. 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 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