Alignments for a candidate for acnD in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudomonas fluorescens FW300-N2C3

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate AO356_20875 AO356_20875 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20875
          Length = 863

 Score = 1442 bits (3734), Expect = 0.0
 Identities = 725/860 (84%), Positives = 776/860 (90%), Gaps = 1/860 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MNT++RKPLPGT+LDYFD R A++AI PGAY  LPYTSRVLAENLVRRC+P  L  SL Q
Sbjct: 1   MNTEFRKPLPGTSLDYFDVRGAVDAIRPGAYDGLPYTSRVLAENLVRRCDPATLRESLLQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           +IE K++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPAQVNPVVPTQLIVDH
Sbjct: 61  LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE GG D  AFAKNRAIEDRRNEDRFHFINWT+KAFKN+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVESGGADPQAFAKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVI  R+GVAFPDT VGTDSHTPHVDALGVIAIGVGGLEAESVMLGRAS+MRLP+I+GV
Sbjct: 181 SPVIQQRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPEIVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           ELTGK QPGITATD+VLALTEFLR QKVV ++LEFFGEGA ALTLGDR TISNM PE+GA
Sbjct: 241 ELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRVTISNMAPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TAAMF+IDQQT+DYL LTGRE  QV+LVETYAK  GLW+D LK A Y R L FDLSSVVR
Sbjct: 301 TAAMFHIDQQTIDYLKLTGREDTQVQLVETYAKHVGLWADSLKGAQYERGLTFDLSSVVR 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424
            +AGPSNPHARV  SELAA+GISG+ ++ PG MPDGAVIIAAITSCTNTSNPRNVIAAGL
Sbjct: 361 NMAGPSNPHARVAVSELAAKGISGQWDDVPGQMPDGAVIIAAITSCTNTSNPRNVIAAGL 420

Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484
           LARNAN  GL RKPWVK+SLAPGSK V LYL+EA L  ELE LGFG+V FACTTCNGMSG
Sbjct: 421 LARNANRLGLARKPWVKSSLAPGSKTVALYLDEAGLTSELEKLGFGVVAFACTTCNGMSG 480

Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544
           ALDPVIQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE
Sbjct: 481 ALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540

Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604
           KDVLG+  DG+ +RL +IWPSD EIDAV+ ASVKPEQFR+VY PMF +  D G KV+PLY
Sbjct: 541 KDVLGV-VDGREIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIQEDTGPKVTPLY 599

Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664
           DWRPQSTYIRRPPYWEGALAG R LKGMRPLAVL DNITTDHLSPSNAIM+DSAAGEYL 
Sbjct: 600 DWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLA 659

Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRM 724
           KMGLPEEDFNSYATHRGDHLTAQRATFANPKL NEM   +GKVKQGSLAR+EPEG V RM
Sbjct: 660 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEGKVMRM 719

Query: 725 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 784
           WEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAI AEGFERIHRTNLVGMG
Sbjct: 720 WEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLVGMG 779

Query: 785 VLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 844
           VLPLEFK G +R T GIDG+EV+DVIG   PRA LT++ITRKNGERVEVPVTCRLDTAEE
Sbjct: 780 VLPLEFKPGTDRKTLGIDGSEVYDVIGERTPRATLTLVITRKNGERVEVPVTCRLDTAEE 839

Query: 845 VSIYEAGGVLQRFAQDFLES 864
           VSIYEAGGVLQRFAQDFLES
Sbjct: 840 VSIYEAGGVLQRFAQDFLES 859


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: 2248
Number of extensions: 94
Number of successful extensions: 2
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: 863
Length adjustment: 42
Effective length of query: 825
Effective length of database: 821
Effective search space:   677325
Effective search space used:   677325
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.

Downloads

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, 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