Alignments for a candidate for acnD in Sphingomonas wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Sphingomonas wittichii RW1

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_012048939.1 SWIT_RS13825 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000016765.1:WP_012048939.1
          Length = 894

 Score =  715 bits (1845), Expect = 0.0
 Identities = 397/862 (46%), Positives = 533/862 (61%), Gaps = 49/862 (5%)

Query: 33  GAYAKLPYTSRVLAENLVRRCEPEMLTASLKQII-----ESKQELDFPWFPARVVCHDIL 87
           G  ++LP++ +VL ENL+R  +   +T    Q I     E   E +  + PARV+  D  
Sbjct: 35  GDISRLPFSMKVLLENLLRFEDGTTVTTEDVQAIVDWQKERTSEREIQYRPARVLMQDFT 94

Query: 88  GQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDR 147
           G   +VDLA +RDA+   GGD  ++NP+VP  L++DHS+ V+  G  K AF +N A+E  
Sbjct: 95  GVPCVVDLAAMRDAMNTLGGDAQKINPLVPVHLVIDHSVMVDSFGSPK-AFDENVALEYA 153

Query: 148 RNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNG-----VAFPDTLVG 202
           RN +R+ F+ W  KA  N  V+P G GI HQ+NLE ++  + +        VA+PDT VG
Sbjct: 154 RNGERYEFLRWGSKALNNFKVVPPGTGICHQVNLENLAQAVWSSADGSGVEVAYPDTCVG 213

Query: 203 TDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLA 262
           TDSHT  ++ LGV+  GVGG+EAE+ MLG+   M +P+++G +L+G    GITATD+VL 
Sbjct: 214 TDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVVGFKLSGTLTEGITATDLVLT 273

Query: 263 LTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLT 322
           +T+ LRA+ VV  ++EF+G G +AL+L DRATI+NM PE+GAT   F ID  TL Y+ LT
Sbjct: 274 VTQMLRAKGVVGRFVEFYGPGLDALSLADRATIANMAPEYGATCGFFPIDDATLVYMRLT 333

Query: 323 GREAEQVKLVETYAKTAGLWSD-DLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVP---- 377
           GR AE V LVE YAK  G W D      V+  TLH D+S+V  ++AGP  P  RV     
Sbjct: 334 GRSAETVALVEAYAKEQGFWRDATAADPVFTDTLHLDMSTVQPSLAGPKRPQDRVLLASV 393

Query: 378 ----TSELAARGISGE-------VENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLA 426
                SELA     G+       VE     +  G V+IAAITSCTNTSNP  ++AAGL+A
Sbjct: 394 DEGFNSELATGYKKGDEADKRVAVEGTGFDIGHGDVVIAAITSCTNTSNPSVLVAAGLVA 453

Query: 427 RNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGAL 486
           R ANA GL  KPWVKTSLAPGS+ V  YLE+A L  +L+++GF +VG+ CTTC G SG L
Sbjct: 454 RKANALGLKAKPWVKTSLAPGSQVVTDYLEKAGLQKDLDAIGFNLVGYGCTTCIGNSGPL 513

Query: 487 DPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKD 546
              I + +   DL A+AVLSGNRNF+GR+ P  +  +LASPPLVVAYA+ GT   DI ++
Sbjct: 514 PDPISKAINGNDLVASAVLSGNRNFEGRVSPDVRANYLASPPLVVAYALFGTTARDITQE 573

Query: 547 VLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDK------- 599
            +G   D KPV L +IWP+ AE+   +AA++  E F   Y  +F      GDK       
Sbjct: 574 PIGTSSDDKPVYLKDIWPTTAEVANTVAAAIDSEMFSSRYANVFQ-----GDKNWQAIDV 628

Query: 600 -VSPLYDWRPQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMM 655
             S  Y WR  STY+  PPY+EG     A  R +   RPLA+  D+ITTDH+SP+ +I +
Sbjct: 629 EGSDTYAWRAGSTYVANPPYFEGMSMTPAPVRDIVEARPLAIFADSITTDHISPAGSIKV 688

Query: 656 DSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARI 715
           DS AG YL +  + + DFNSY   RG+H    R TFAN ++KN+M  + G   +G L + 
Sbjct: 689 DSPAGRYLTEHQVTKADFNSYGARRGNHEVMMRGTFANIRIKNQM--IPG--IEGGLTKH 744

Query: 716 EPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERI 775
            P G V  +++A   Y     PL+++AG +YG GSSRDWAAKG  L GV A++AE FERI
Sbjct: 745 IPSGEVMAIYDAAMKYKAEGTPLVVVAGKEYGTGSSRDWAAKGTNLLGVRAVIAESFERI 804

Query: 776 HRTNLVGMGVLPLEFKAGENRATYGIDGTEVF--DVIGSIAPRADLTVIITRKNGERVEV 833
           HR+NLVGMGVLPL+F  G +R T  +DGTE F  D +  + PR  ++V +TR +G     
Sbjct: 805 HRSNLVGMGVLPLQFAEGIDRNTLKLDGTETFSIDDVAGLRPRQTVSVKLTRADGSTESF 864

Query: 834 PVTCRLDTAEEVSIYEAGGVLQ 855
              CR+DT  E+  +  GG+LQ
Sbjct: 865 ETRCRIDTVNELEYFLNGGILQ 886


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: 1914
Number of extensions: 96
Number of successful extensions: 10
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: 894
Length adjustment: 43
Effective length of query: 824
Effective length of database: 851
Effective search space:   701224
Effective search space used:   701224
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