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

GapMind for catabolism of small carbon sources

Aligments 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:

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, or view the source code.

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