GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Algiphilus aromaticivorans DG1253

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_043766717.1 U743_RS06915 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000733765.1:WP_043766717.1
          Length = 883

 Score =  727 bits (1876), Expect = 0.0
 Identities = 391/851 (45%), Positives = 540/851 (63%), Gaps = 41/851 (4%)

Query: 36  AKLPYTSRVLAENLVRRCEPEMLTASLKQIIESKQELDFP-----WFPARVVCHDILGQT 90
           ++LP++ +VL ENL+R+ + E +T    +   S      P     + PARV+  D  G  
Sbjct: 33  SRLPFSYKVLLENLLRKEDGESVTVEDIETFASADLRKLPAKEIAFTPARVLLQDFTGVP 92

Query: 91  ALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNE 150
            +VDLA +RDA+   GGD  ++NP+ P++L++DHS+ V++ G   D+F  N  +E  RN+
Sbjct: 93  CVVDLAAMRDAMTKLGGDAKKINPLCPSELVIDHSVMVDHYGA-ADSFDLNAKLEFNRNK 151

Query: 151 DRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTLVGTDSHTPHV 210
           +R+ F+ W Q A  N  V+P   GI+HQ+N+E +S V+   +GV +PD+  GTDSHT  V
Sbjct: 152 ERYAFLRWGQNALDNFKVVPPDTGIVHQVNIEYLSRVVFDNDGVLYPDSCFGTDSHTTMV 211

Query: 211 DALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQ 270
           + LGV+  GVGG+EAE+ MLG+ S M +P++IGV LTG    G TATD+VL +TE LR +
Sbjct: 212 NGLGVLGWGVGGIEAEAAMLGQPSTMLMPEVIGVRLTGALPEGATATDLVLTVTEMLRKR 271

Query: 271 KVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVK 330
            VV  ++EFFG+G   LTL DRATI+NM PE+GAT  +F ID++TL YL LTGR  +QV+
Sbjct: 272 GVVEKFVEFFGDGLSELTLADRATIANMAPEYGATCGIFPIDEETLKYLRLTGRTEDQVE 331

Query: 331 LVETYAKTAGLWSDDLK-QAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSEL-------- 381
           +V+ YA+  G+W +  + +A Y   LH +L S+  ++AGP  P  RV  S++        
Sbjct: 332 VVKAYAQAQGMWREKGEPEAEYSDVLHLELGSIQPSLAGPKRPQDRVLLSDVQANYQQAF 391

Query: 382 ----AARGISGEV----ENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKG 433
               A R   G      +++   + DG V+IAAITSCTNTSNP  +I AGLLARNA AKG
Sbjct: 392 EADQAGRPTKGSAKVNYKDQDFQLDDGDVVIAAITSCTNTSNPAVLIGAGLLARNARAKG 451

Query: 434 LTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQE 493
           +T KPWVKTSLAPGSK V  YLE++ LL +LE+LGF +VG+ CTTC G SG L   I + 
Sbjct: 452 ITVKPWVKTSLAPGSKVVTDYLEKSGLLEDLEALGFYVVGYGCTTCIGNSGPLPEPIAEA 511

Query: 494 VIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKD 553
           V   +L   +VLSGNRNF+GR+H   +  +LASPPLVVAYA+AG++  D+ KD +G + D
Sbjct: 512 VTANNLSVASVLSGNRNFEGRVHQDVRMNYLASPPLVVAYALAGSVDIDLNKDPIGENTD 571

Query: 554 GKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFD-------LSVDYGDKVSPLYDW 606
           G+PV L +IWP   EI  +IA+S+  E F   Y  +FD       L V  GD+    Y+W
Sbjct: 572 GQPVYLKDIWPKSQEIQDLIASSLNAEMFTTSYGKVFDGDDRWRGLDVPTGDR----YEW 627

Query: 607 RPQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYL 663
           R  STY++ PPY+EG    + G   +K  R LA+LGD++TTDH+SP+ AI  DS AG+YL
Sbjct: 628 RDDSTYVQNPPYFEGMTKEVPGLPAIKSARVLALLGDSVTTDHISPAGAIKQDSPAGKYL 687

Query: 664 HKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTR 723
            + G+   DFNSY + RG+H    R TFAN +++N+M  V G   +G   +  P G    
Sbjct: 688 MENGVKPADFNSYGSRRGNHEVMMRGTFANVRIRNKM--VPG--VEGGYTKHIPSGEQMA 743

Query: 724 MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 783
           +++A   Y      L++IAG +YG GSSRDWAAKG  L G +A++AE FERIHR+NLVGM
Sbjct: 744 IYDAAMKYQAEGTQLVVIAGKEYGTGSSRDWAAKGTNLLGAKAVIAESFERIHRSNLVGM 803

Query: 784 GVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAE 843
           GV+PL FK G+N    G+DG+E  D+ G      ++TV   + NGE V      R+DT +
Sbjct: 804 GVVPLTFKDGQNAENLGLDGSEQIDIEGLEQGAKEVTVKAHKDNGETVTFTARVRIDTPK 863

Query: 844 EVSIYEAGGVL 854
           E      GGVL
Sbjct: 864 EWEYNRHGGVL 874


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: 1895
Number of extensions: 85
Number of successful extensions: 8
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: 883
Length adjustment: 42
Effective length of query: 825
Effective length of database: 841
Effective search space:   693825
Effective search space used:   693825
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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