Alignments for a candidate for acnD in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Paraburkholderia bryophila 376MFSha3.1

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate H281DRAFT_06210 H281DRAFT_06210 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Burk376:H281DRAFT_06210
          Length = 898

 Score =  712 bits (1838), Expect = 0.0
 Identities = 386/872 (44%), Positives = 533/872 (61%), Gaps = 41/872 (4%)

Query: 18  LDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQIIESKQELDFPWF 77
           L Y D + A EA      ++LP + R+L EN +RR   + + A    +   + + +  +F
Sbjct: 21  LRYADLKRA-EAQGFAPLSELPVSLRILLENAMRRGGVDDVAAIRDWLTRRESDREISFF 79

Query: 78  PARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDA 137
           P RV+  D      + DLA +RDA+  KGGD  +VNP++P  ++VDHS   ++ G   DA
Sbjct: 80  PVRVLMPDSSAVPLVADLAAMRDAVRKKGGDSWRVNPLIPVDIVVDHSAITDHAG-RSDA 138

Query: 138 FAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR--NGVA 195
           F  N A+E +RN +R+ F+ W Q AF N+ V+P   GI+HQ+NLE ++  +     + V 
Sbjct: 139 FDLNLALEYQRNHERYAFLKWAQNAFDNVRVVPPATGIVHQVNLEFLAAGVQTVVIDDVT 198

Query: 196 F--PDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPG 253
           F  PDTLVG DSHT  V+++GV+  GVGG+EA + +LG+   M LP +IG  ++G+P+ G
Sbjct: 199 FVVPDTLVGMDSHTTMVNSIGVLGWGVGGIEAAAAILGQPISMLLPRVIGCRISGRPRSG 258

Query: 254 ITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQ 313
           +T TDIVL+LTEFLR +KVV  ++EFFGEG + L + DRATI+NM PE GAT   F  D 
Sbjct: 259 VTCTDIVLSLTEFLRGKKVVGCFVEFFGEGLDNLPVSDRATIANMAPEAGATMCFFPPDA 318

Query: 314 QTLDYLTLTGREAEQVKLVETYAKTAGLWSD----DLKQAVYPRTLHFDLSSVVRTIAGP 369
            T++YL  TGR  EQV + E   K  G+W      D ++  Y   L FDLS+V  ++AGP
Sbjct: 319 ATIEYLHATGRSREQVAVAEAVLKAQGIWRPEAGADEERIAYSDRLEFDLSAVTPSMAGP 378

Query: 370 SNPHARVPTSELAAR-----GISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424
             P  RV   +++AR     G++ E       + +G+V+IAAITSCTNTSN R +I AGL
Sbjct: 379 KRPQDRVDLKDVSARFHREFGLTAEGRG----LTNGSVVIAAITSCTNTSNARAMIGAGL 434

Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484
           +ARN  A+G+  K WVKTSL+PGS+ V  YL E+ L  +L+SLGF + G+ C TC G SG
Sbjct: 435 IARNLRARGVKPKAWVKTSLSPGSRVVTDYLRESGLQDDLDSLGFNLTGYGCMTCAGSSG 494

Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544
            LD  + + ++   L    VLSGNRNF+GR HP A+  FL SP LVVAYA AGTI  D+ 
Sbjct: 495 QLDAEVARRILSEGLVVATVLSGNRNFEGRTHPLARANFLGSPALVVAYACAGTILRDLT 554

Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFD-------LSVDYG 597
            + +  + DG+PV L ++WP DA+IDA+    V    F++VY   F        ++   G
Sbjct: 555 TEPIADEADGQPVMLADVWPDDADIDAIFRRIVTLTMFKRVYATAFQGEARWQRIAAASG 614

Query: 598 DKVSPLYDWRPQSTYIRRPPYWEGALA----GERTLKGMRPLAVLGDNITTDHLSPSNAI 653
           D     +DW   STYIRRPPY++   A    G   + G R L +LGD+ITTDH+SP   I
Sbjct: 615 DH----FDWDQASTYIRRPPYFDAGFADDGFGMANIVGARALLMLGDSITTDHISPVGVI 670

Query: 654 MMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLA 713
             ++ AG +LH  G+   DFN+  + R +H    R TFAN +L+NEM       ++G  +
Sbjct: 671 RSETEAGRFLHGAGVAPSDFNTLLSRRANHDVMMRGTFANVRLRNEMT----PDREGPWS 726

Query: 714 RIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFE 773
           R  P G V R+++A   Y D + PLI+IAGADYG GSSRDWAAKG RL GV A++AE FE
Sbjct: 727 RHVPSGDVMRVFQAASRYRDERVPLIVIAGADYGAGSSRDWAAKGPRLLGVRAVIAESFE 786

Query: 774 RIHRTNLVGMGVLPLEFKAGENRATYGIDGTE---VFDVIGSIAPRADLTVIITRKNGER 830
           RIHR+NLVGMG+LPL+F  G  R T G+ G E   +F + G++ P   +   ++R NG R
Sbjct: 787 RIHRSNLVGMGILPLQFPPGTTRKTLGLTGEESFTIFGIEGALQPHQRIECEVSRANGAR 846

Query: 831 VEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFL 862
             + + CRLD   E++ Y  GGVLQ  A   L
Sbjct: 847 DSITLICRLDIPREIAWYRHGGVLQYIAAQLL 878


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: 1925
Number of extensions: 95
Number of successful extensions: 9
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: 898
Length adjustment: 43
Effective length of query: 824
Effective length of database: 855
Effective search space:   704520
Effective search space used:   704520
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