Aligments for a candidate for acnD in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for acnD in Acidovorax sp. GW101-3H11

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate Ac3H11_1140 Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1140
          Length = 980

 Score =  613 bits (1580), Expect = e-179
 Identities = 365/934 (39%), Positives = 528/934 (56%), Gaps = 109/934 (11%)

Query: 37  KLPYTSRVLAENLVRRCE-----PEMLTASLKQIIESKQELDFPWFPARVVCHDILGQTA 91
           +LP + R++ E+++R C+     PE +    +    ++++ + P+  +RVV  D  G   
Sbjct: 48  RLPVSIRIVLESVLRNCDGRKVTPEHVEQLARWAPNAERKDEIPFVVSRVVLQDFTGVPL 107

Query: 92  LVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNED 151
           L DLA +R   A  G +P ++ P+VP  L+VDHS+ +++ G  K++   N  +E +RN +
Sbjct: 108 LADLAAMRSVAAKLGKNPKKIEPLVPVDLVVDHSIMIDHYG-KKNSLDLNMKLEFQRNRE 166

Query: 152 RFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR-NGVAFPDTLVGTDSHTPHV 210
           R+ F+ W  +AF    V+P G GI+HQ+NLE ++  +H R +GV +PDTLVGTDSHT  +
Sbjct: 167 RYEFMKWGMQAFDTFGVVPPGFGIVHQVNLEYLARGVHKRKDGVFYPDTLVGTDSHTTMI 226

Query: 211 DALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQ 270
           + +GV+  GVGG+EAE+ MLG+  Y   PD++G E+TG+ + G+TATD+VL +TE LR  
Sbjct: 227 NGIGVVGWGVGGIEAEAAMLGQPVYFLTPDVVGFEMTGRLREGVTATDLVLTVTELLRKH 286

Query: 271 KVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVK 330
           KVV  ++EFFGEG   L L DRATI NM PE+GAT   F +D++T+DY   TGR   +++
Sbjct: 287 KVVGKFVEFFGEGTRTLALPDRATIGNMAPEYGATMGFFPVDEKTIDYFQGTGRTKAEIE 346

Query: 331 LVETYAKTAGLWSDDLKQAV-YPRTLHFDLSSVVRTIAGPSNPHARVPT-------SELA 382
             E Y K  GL+   L   V Y + +  DL SV  ++AGP  P  R+         ++L 
Sbjct: 347 AFEAYFKAQGLFGVPLAGEVDYSQVVTLDLGSVTPSLAGPKRPQDRIELGQVSRQFADLF 406

Query: 383 ARGISGEVENEPGLM-------PDGAVIIAAIT---SCTNTSNPRNVI------------ 420
           ++  +    N P  +          A ++A +T     T    PR+V+            
Sbjct: 407 SQPAAHNGFNRPAELLHTRFHIHRAAEVVADVTPDGKPTPAGAPRSVVEMEANKPALATA 466

Query: 421 -----AAGLLARNAN--------------------------AKGLTRKPWVK-------- 441
                +A L AR A+                          A GL  K  V+        
Sbjct: 467 HAEARSATLPARGADPTVGNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPH 526

Query: 442 --TSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDL 499
             TSLAPGS+ V  YL E  LLP LE LGF I G+ CTTC G +G L P + + +   DL
Sbjct: 527 IKTSLAPGSRIVTEYLSETGLLPYLEKLGFSIAGYGCTTCIGNAGDLTPELNEAITQNDL 586

Query: 500 YATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRL 559
              AVLSGNRNF+ RIHP  K  FLASPPLVVAYAIAGT+  D+  + +G  K GK + L
Sbjct: 587 VCAAVLSGNRNFEARIHPNLKANFLASPPLVVAYAIAGTVLKDLMTEPVGQGKGGKDIYL 646

Query: 560 INIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPL----YDWRPQSTYIRR 615
            +IWPS  E+ A++  ++K + FR  Y  +        +K+  +    Y W P STYI  
Sbjct: 647 GDIWPSSDEVHALLKFAMKGKAFRDNYAKVATDPGKLWEKIQGVSGTAYTW-PASTYIAE 705

Query: 616 PPYW------EGA--LAGER----------TLKGMRPLAVLGDNITTDHLSPSNAIMMDS 657
           PP++      +GA   +G R          ++ G R +A+ GD+ITTDH+SP+ +I   S
Sbjct: 706 PPFFAQFALEKGANKASGTRGEGQKDAQLPSVMGARIMALFGDSITTDHISPAGSIKESS 765

Query: 658 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM--AIVDGKVKQGSLARI 715
            AG++L + G+ + DFNSY   RG+H    R TFAN ++KN M     DG  ++G +   
Sbjct: 766 PAGQWLLQHGVQKADFNSYGARRGNHDVMVRGTFANVRIKNLMIPPTADGSREEGGVTVF 825

Query: 716 EPEGIVTR----MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEG 771
           + EG +      +++A   YM +  P ++ AG +YG GSSRDWAAKG +L G++A+VA  
Sbjct: 826 QNEGALQGEKMFIFDAAMQYMAQGTPTVVFAGEEYGTGSSRDWAAKGTQLLGIKAVVARS 885

Query: 772 FERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVI--GSIAPRADLTVIITRKNGE 829
           FERIHR+NLVGMGVLPL+FKAG++  T G+ G EV DV+   ++ P++D  ++I R +G 
Sbjct: 886 FERIHRSNLVGMGVLPLQFKAGDSWETLGLTGNEVIDVLPDPALTPQSDARLVIRRADGT 945

Query: 830 RVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 863
             EV VT R+DT  EV  Y AGG+L    +  LE
Sbjct: 946 VREVVVTLRIDTPIEVDYYRAGGILPFVLRQLLE 979


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: 2096
Number of extensions: 113
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 867
Length of database: 980
Length adjustment: 43
Effective length of query: 824
Effective length of database: 937
Effective search space:   772088
Effective search space used:   772088
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: 57 (26.6 bits)

This GapMind analysis is from Sep 17 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, or view the source code.

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