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_06606 H281DRAFT_06606 aconitase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Burk376:H281DRAFT_06606
          Length = 905

 Score =  647 bits (1670), Expect = 0.0
 Identities = 355/861 (41%), Positives = 521/861 (60%), Gaps = 45/861 (5%)

Query: 37  KLPYTSRVLAENLVRRCEPEMLTAS-LKQIIESKQEL----DFPWFPARVVCHDILGQTA 91
           +LP + R++ E+++R  + + +    + Q+   K       + P+  +RVV  D  G   
Sbjct: 37  RLPVSIRIVLESVLRNYDGKKIAEEHITQLANWKPTAPRVDEIPFVVSRVVLQDFTGVPL 96

Query: 92  LVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNED 151
           L D+A +R      G +P  + P+VP  L+VDHS+ +++   +K+A   N  +E +RN +
Sbjct: 97  LADIAAMRGVAQRVGKNPKSIEPLVPVDLVVDHSVQIDHFR-EKNALDLNMKLEFQRNNE 155

Query: 152 RFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR----NGVAFPDTLVGTDSHT 207
           R+ F+ W  +AF    V+P G GI+HQ+NLE ++  +H +    + V +PD+LVGTDSHT
Sbjct: 156 RYQFMKWGMQAFDTFKVVPPGVGIVHQVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHT 215

Query: 208 PHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFL 267
             ++ +GV+  GVGG+EAE+ MLG+  Y   PD++GV L GK + G+TATD+VL +TE L
Sbjct: 216 TMINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDVVGVNLKGKLREGVTATDLVLTITELL 275

Query: 268 RAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAE 327
           R +KVV  ++EFFGEG  +L+L DRATI NM PE+GAT   F +D++T+DY   TGR   
Sbjct: 276 RKEKVVGKFVEFFGEGTRSLSLPDRATIGNMAPEYGATMGFFPVDEKTIDYFKGTGRTDA 335

Query: 328 QVKLVETYAKTAGLWSDDLKQAV-YPRTLHFDLSSVVRTIAGPSNPHARVPT-------S 379
           ++   + Y K   L+    +  + + + +  DL +V  ++AGP  P  R+         S
Sbjct: 336 EISAFQNYFKAQNLFGIPKEGDIDFTKVVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTFS 395

Query: 380 ELAARGIS--GEVENEPGL-----------MPDGAVIIAAITSCTNTSNPRNVIAAGLLA 426
           +L ++ ++  G  + E  L           + +G V+IAAITSCTNTSNP  ++AAGLLA
Sbjct: 396 DLFSKPVAENGFAKKEADLDAQYTTSNGVNVKNGDVLIAAITSCTNTSNPSVLLAAGLLA 455

Query: 427 RNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGAL 486
           + A   GLT  P +KTSLAPGS+ V  YL +  LLP L+ LGF +  + CTTC G +G L
Sbjct: 456 KKAVEAGLTVAPHIKTSLAPGSRIVTEYLTKTGLLPYLDKLGFTLAAYGCTTCIGNAGDL 515

Query: 487 DPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKD 546
            P + + +   D+ A AVLSGNRNF+ RIHP  +  FLASPPLVVAYAIAG I  D+  +
Sbjct: 516 TPELNEAITKNDIVAAAVLSGNRNFEARIHPNIRANFLASPPLVVAYAIAGNITRDLMTE 575

Query: 547 VLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMF---DLSVDYGDKVSPL 603
            +G  K GK V L +IWP+  E++ ++  ++  + FRK Y  +    DL      +   +
Sbjct: 576 PVGKGKGGKDVYLGDIWPTSDEVNDLLKFALDADAFRKNYASLTKKGDLWSKIEGEEGQV 635

Query: 604 YDWRPQSTYIRRPPYWEGALA-----GERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSA 658
           YDW P+STYI  PP++    +         +K  R L + GD++TTDH+SP+ +I  DS 
Sbjct: 636 YDW-PKSTYIAEPPFFGNDFSMTPADSIAAVKNARALGIFGDSVTTDHISPAGSIKEDSP 694

Query: 659 AGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM--AIVDGKVKQGSLARIE 716
           AG++L + G+ + DFNSY + RG+H    R TFAN ++KN M  A  DG   +G L   +
Sbjct: 695 AGKWLKENGVQKADFNSYGSRRGNHDVMMRGTFANVRIKNLMIPAKADGSRVEGGLTIHQ 754

Query: 717 PEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIH 776
           P G    +++A   Y+D   P I+ AG +YG GSSRDWAAKG +L GV+A+VA  FERIH
Sbjct: 755 PSGEQLSIYDAAMKYIDAGTPTIVFAGEEYGTGSSRDWAAKGTQLLGVKAVVARSFERIH 814

Query: 777 RTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG---SIAPRADLTVIITRKNGERVEV 833
           R+NLVGMGVLPL+FK  ++  + GI G E +D+ G      P+ ++T++I  K+G    V
Sbjct: 815 RSNLVGMGVLPLQFKGSDSVQSLGITGEETYDIEGLGADFKPQQEVTLVIRGKDGSEKRV 874

Query: 834 PVTCRLDTAEEVSIYEAGGVL 854
           PV  R+DT  EV  Y+ GG+L
Sbjct: 875 PVLLRIDTPIEVDYYKHGGIL 895


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: 1948
Number of extensions: 111
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: 905
Length adjustment: 43
Effective length of query: 824
Effective length of database: 862
Effective search space:   710288
Effective search space used:   710288
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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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 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