Alignments for a candidate for acnD in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Caulobacter crescentus NA1000

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate CCNA_03781 CCNA_03781 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Caulo:CCNA_03781
          Length = 895

 Score =  656 bits (1693), Expect = 0.0
 Identities = 378/870 (43%), Positives = 523/870 (60%), Gaps = 42/870 (4%)

Query: 20  YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS-LKQII-----ESKQELD 73
           Y+  R A EA      + LP + +VL ENL+R  +   +    LK +      +   E +
Sbjct: 22  YYSLRAAEEA-GLADVSSLPVSMKVLLENLLRNEDGVSVNEDDLKAVAAWLNNKGSVEHE 80

Query: 74  FPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGF 133
             + PARV+  D  G  A+VDLA +RDA+ A G DPA++NP+ P  L++DHS+ V+  G 
Sbjct: 81  ISFRPARVLMQDFTGVPAVVDLAAMRDAMVALGADPAKINPLNPVDLVIDHSVMVDNFGN 140

Query: 134 DKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARN- 192
            K A+  N   E  RN +R+ F+ W   AF N  V+P G GI HQ+NLE ++  +     
Sbjct: 141 PK-AYDDNVKREYERNIERYRFLRWGSSAFNNFRVVPPGTGICHQVNLEYLAQTVWTNTV 199

Query: 193 ---GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGK 249
               VA+PDT+VGTDSHT  V+ L V+  GVGG+EAE+ MLG+   M +P++IG +LTG 
Sbjct: 200 DGAEVAYPDTVVGTDSHTTMVNGLAVLGWGVGGIEAEAAMLGQPIPMLIPEVIGFKLTGA 259

Query: 250 PQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMF 309
              G TATD+VL +T+ LR + VV  ++EF+G+    LTL D+ATI+NM PE+GAT   F
Sbjct: 260 MPEGATATDLVLTVTQMLRKKGVVGKFVEFYGDALANLTLEDQATIANMAPEYGATCGFF 319

Query: 310 YIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDD-LKQAVYPRTLHFDLSSVVRTIAG 368
            I   T+ YL  TGR AE+V LVE YAK  GLW +  + +  +  TL  DLS+V+ ++AG
Sbjct: 320 PISAATIAYLKGTGRAAERVALVEAYAKEQGLWWEPGVAEPTFTDTLELDLSTVLPSLAG 379

Query: 369 PSNPHARVPTSELAAR---GISGE------------VENEPGLMPDGAVIIAAITSCTNT 413
           P  P  RV  S+ AA+    ++GE            VE E   +  G V+IAAITSCTNT
Sbjct: 380 PKRPQDRVLLSDAAAKFAESLAGEFGKAENPELRAPVEGEDFDVGHGDVVIAAITSCTNT 439

Query: 414 SNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVG 473
           SNP  +IAAGLLA+NA AKGL  KPWVKTSLAPGS+ V  YL +A L   L++LGF +VG
Sbjct: 440 SNPSVLIAAGLLAKNAVAKGLKAKPWVKTSLAPGSQVVTDYLAKAGLTKHLDALGFNLVG 499

Query: 474 FACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAY 533
           + CTTC G SG L   I + + D DL A +VLSGNRNF+GR++P  +  +LASPPLVVAY
Sbjct: 500 YGCTTCIGNSGPLPEAISKTINDNDLVACSVLSGNRNFEGRVNPDVRANYLASPPLVVAY 559

Query: 534 AIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLS 593
           A+AG+++ D+    +G DK G  V L +IWPS+ +I A+   ++  + F   Y  +F   
Sbjct: 560 ALAGSLKIDLATQPIGQDKKGNDVFLKDIWPSNEDIAALQRKAINEKMFATRYGDVFKGD 619

Query: 594 VDY-GDKVS--PLYDWRPQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGDNITTDHL 647
            ++ G KV+    Y W   STY++ PPY+       A    +   R LAV GD+ITTDH+
Sbjct: 620 KNWQGIKVTGGQTYAWEADSTYVQNPPYFPNMSMTPAPVTDIVEARILAVFGDSITTDHI 679

Query: 648 SPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKV 707
           SP+ +I   S AG++L   G+   DFN Y   RG+H    R TFAN +++N +       
Sbjct: 680 SPAGSIKASSPAGKFLIDNGVEPVDFNGYGARRGNHQVMMRGTFANIRIRNRIT----PD 735

Query: 708 KQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAI 767
            +G + +  P G V  +++A   Y +  +P ++  G +YG GSSRDWAAKG +L GV A+
Sbjct: 736 IEGGVTKHFPTGEVMSIYDAAMKYQEEGRPAVVFGGKEYGTGSSRDWAAKGTKLLGVRAV 795

Query: 768 VAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG--SIAPRADLTVIITR 825
           + E FERIHR+NLVGMGVLPL+F   +      + G E+  + G   +APR  L V + R
Sbjct: 796 ICESFERIHRSNLVGMGVLPLQF-VQDGWQKLELTGEEIVSIRGLTDLAPRKQLIVELYR 854

Query: 826 KNGERV-EVPVTCRLDTAEEVSIYEAGGVL 854
               R+   PV CR+DT  E+  ++ GGVL
Sbjct: 855 PTDGRIARFPVRCRIDTPTELEYFKNGGVL 884


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: 1916
Number of extensions: 90
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: 895
Length adjustment: 43
Effective length of query: 824
Effective length of database: 852
Effective search space:   702048
Effective search space used:   702048
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 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
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