Alignments for a candidate for acnD in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Paraburkholderia phymatum STM815

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_041765781.1 BPHY_RS33395 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000020045.1:WP_041765781.1
          Length = 865

 Score = 1478 bits (3827), Expect = 0.0
 Identities = 732/861 (85%), Positives = 791/861 (91%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MNT YRKPLPGT+LDYFDTR A++AI PGAY KLPYTSRV AENLVRRC+P  L  SLKQ
Sbjct: 1   MNTAYRKPLPGTSLDYFDTRAAVDAIQPGAYDKLPYTSRVHAENLVRRCDPATLNDSLKQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           I+E K+ELDFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPA+VNPVVP QLIVDH
Sbjct: 61  IVERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE GGFD DAFAKNRAIEDRRNEDRF FINWT+KAFKN+DVIP GNGIMHQINLERM
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFDFINWTKKAFKNVDVIPPGNGIMHQINLERM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVIHA +GVA+PDTLVGTDSHTPHVDALGVIA+GVGGLEAE+VMLGRAS+MRLPDI+GV
Sbjct: 181 SPVIHAADGVAYPDTLVGTDSHTPHVDALGVIAVGVGGLEAENVMLGRASWMRLPDIVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           EL+GK QPGITATDIVLALTEFLR +KVV +YLEF GEGA +LTLGDRATISNM PE+GA
Sbjct: 241 ELSGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TAAMF+ID+QT+DYL LTGR+  QVKLVETYAKTAGLW+D LK A Y R L FDLS+VVR
Sbjct: 301 TAAMFFIDEQTIDYLRLTGRDDAQVKLVETYAKTAGLWADTLKHAEYERILSFDLSTVVR 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424
            +AGPSNPH R+PTS+LA RGI+G+ E  PG MPDGAVIIAAITSCTNTSNPRNVIAA L
Sbjct: 361 NMAGPSNPHRRLPTSDLAERGIAGKWEEVPGQMPDGAVIIAAITSCTNTSNPRNVIAAAL 420

Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484
           LARNANA+GLTRKPWVK+SLAPGSKAV+LYL+EANLLPELE LGFGIV FACTTCNGMSG
Sbjct: 421 LARNANARGLTRKPWVKSSLAPGSKAVELYLQEANLLPELEKLGFGIVAFACTTCNGMSG 480

Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544
           ALDP IQQE++DRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE
Sbjct: 481 ALDPAIQQEIVDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540

Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604
           +DVLG D+DGKPV L +IWPSD EIDA++  SVKPEQFRKVYEPMF ++   G+ +SPLY
Sbjct: 541 RDVLGTDRDGKPVYLKDIWPSDEEIDAIVKQSVKPEQFRKVYEPMFAVTAASGEPISPLY 600

Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664
           DWR QSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAI+ +SAAGEYL 
Sbjct: 601 DWRAQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILANSAAGEYLT 660

Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRM 724
           KMGLPEEDFNSYATHRGDHLTAQRATFANP L NEMA+VDG++K+GSLARIEPEG VTRM
Sbjct: 661 KMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQLKKGSLARIEPEGKVTRM 720

Query: 725 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 784
           WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNL+GMG
Sbjct: 721 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLIGMG 780

Query: 785 VLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 844
           VLPLEFK G NR   GIDGTE +DVIG   PRADLT++I RKNGERV+VPVTCRLDTAEE
Sbjct: 781 VLPLEFKRGVNRLALGIDGTETYDVIGERRPRADLTLVIHRKNGERVDVPVTCRLDTAEE 840

Query: 845 VSIYEAGGVLQRFAQDFLESN 865
           VSIYEAGGVLQRFAQDFLES+
Sbjct: 841 VSIYEAGGVLQRFAQDFLESS 861


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: 2308
Number of extensions: 100
Number of successful extensions: 1
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: 865
Length adjustment: 42
Effective length of query: 825
Effective length of database: 823
Effective search space:   678975
Effective search space used:   678975
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 Apr 09 2024. 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 2024 update 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