GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Bacteroides thetaiotaomicron VPI-5482

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate 351600 BT2072 aconitate hydratase (NCBI ptt file)

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Btheta:351600
          Length = 747

 Score =  214 bits (544), Expect = 2e-59
 Identities = 223/765 (29%), Positives = 331/765 (43%), Gaps = 116/765 (15%)

Query: 78  PARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDA 137
           P RV   D   Q AL+              +  +    VP+ +  DH L   Y G  +D 
Sbjct: 61  PDRVAMQDATAQMALLQFM-----------NAGKEKVAVPSTVHCDH-LIQAYKGAKEDI 108

Query: 138 FAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFP 197
                A   + NE+ + F+      +  I     G GI+HQ+ LE            AFP
Sbjct: 109 -----ATATKTNEEVYDFLRDVSSRY-GIGFWKPGAGIIHQVVLENY----------AFP 152

Query: 198 D-TLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITA 256
              +VGTDSHTP+   LG++AIGVGG +A  VM G    +++P IIGV LTGK     + 
Sbjct: 153 GGMMVGTDSHTPNAGGLGMVAIGVGGADAVDVMTGMEWELKMPRIIGVRLTGKLSGWTSP 212

Query: 257 TDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTL 316
            D++L L   L  +   +S +E+FG G  +L+   +ATI NM  E GAT ++F  D +  
Sbjct: 213 KDVILKLAGILTVKGGTNSIIEYFGPGTASLSATGKATICNMGAEVGATTSLFPFDGRMA 272

Query: 317 DYLTLTGRE--AEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHA 374
            YL  TGR+   E  + V+   +     +D+  +  Y R +  DLS++   I GP  P A
Sbjct: 273 TYLRATGRDRIVELAEAVDCELRADQQVTDE-PEKYYDRVIDIDLSTLEPYINGPFTPDA 331

Query: 375 RVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGL 434
             P SE A + +   +   P  M      +  I SCTN+S  +++  A  LAR    K L
Sbjct: 332 ATPISEFAEKVL---LNGYPRKME-----VGLIGSCTNSSY-QDLSRAASLARQVKEKNL 382

Query: 435 T-RKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQE 493
           +   P +   + PGS+ ++   E   ++ +   +G  I+  AC  C G         ++ 
Sbjct: 383 SVASPLI---INPGSEQIRATAERDGMMDDFMQIGAVIMANACGPCIGQ-------WKRH 432

Query: 494 VIDRDLYATAVLSGNRNF----DGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLG 549
             D     + V S NRNF    DG  + Y   AF+ASP L +A  IAG + F+  KD L 
Sbjct: 433 TDDPTRKNSIVTSFNRNFAKRADGNPNTY---AFVASPELTMALTIAGDLCFNPLKDRL- 488

Query: 550 LDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLYDWRPQ 609
           ++ DG+ V+L    P   E+             R             G K +   +   Q
Sbjct: 489 MNHDGEKVKLAE--PVGDEL-----------PLRGFTSGNEGYITPGGTKTAINVNPASQ 535

Query: 610 STYIRRP-PYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGL 668
              +  P P W+G     + +  M  L       TTDH+         S AG +L   G 
Sbjct: 536 RLQLLTPFPAWDG-----QDILNMPLLIKAQGKCTTDHI---------SMAGPWLRFRGH 581

Query: 669 PEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAI 728
            E   ++      +    +     N +  N    V G  K       + EGI        
Sbjct: 582 LENISDNMLMGAVNAFNGETNNVWN-RSTNTYGTVSGTAKM-----YKSEGI-------- 627

Query: 729 ETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPL 788
                   P I++A  +YG+GSSR+ AA   R   V  I+A+ F RIH TNL   G+L L
Sbjct: 628 --------PSIVVAEENYGEGSSREHAAMEPRFLNVRVILAKSFARIHETNLKKQGMLAL 679

Query: 789 EFKAGENRATYG-IDGTEVFDVIG--SIAPRADLTVIITRKNGER 830
            F    ++A Y  I   ++  VIG    AP  +LTV++  ++G +
Sbjct: 680 TF---ADKADYDKIQEHDLLSVIGLPDFAPGRNLTVVLHHEDGTK 721


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: 1546
Number of extensions: 87
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 867
Length of database: 747
Length adjustment: 41
Effective length of query: 826
Effective length of database: 706
Effective search space:   583156
Effective search space used:   583156
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