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 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