GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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