Alignments for a candidate for acnD in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudomonas stutzeri RCH2

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate GFF2274 Psest_2319 aconitate hydratase 1/2-methylisocitrate dehydratase, Fe/S-dependent

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__psRCH2:GFF2274
          Length = 867

 Score = 1394 bits (3608), Expect = 0.0
 Identities = 688/865 (79%), Positives = 761/865 (87%), Gaps = 8/865 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MNT++RKPLPGT LDYFDTREAIEAI PG+Y KLPYTSRVLAE LVRRCEPE LT SLKQ
Sbjct: 1   MNTEHRKPLPGTGLDYFDTREAIEAIQPGSYDKLPYTSRVLAEQLVRRCEPEALTDSLKQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           IIE K++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA +GGDPA+VNPVVPTQLIVDH
Sbjct: 61  IIERKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEQGGDPAKVNPVVPTQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE+ GFD DAF KNRA+E+RRNEDRFHFI WT+ AFKN+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVEFAGFDPDAFEKNRAVEERRNEDRFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVI AR GVAFPDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLG  S MRLPDI+GV
Sbjct: 181 SPVIQARGGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVMLGLPSMMRLPDIVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
            LTGK QPGITATDIVLALTEFLR ++VV +++EFFGEGA++LT+GDRATISNM PE+GA
Sbjct: 241 RLTGKRQPGITATDIVLALTEFLRKERVVGAWVEFFGEGADSLTIGDRATISNMCPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TA+MFYIDQQT+DYL LTGRE EQV LVE YAK  GLW+  L+ A Y R L FDLSSVVR
Sbjct: 301 TASMFYIDQQTIDYLKLTGREPEQVALVEQYAKETGLWATALEGAEYERVLEFDLSSVVR 360

Query: 365 TIAGPSNPHARVPTSELAARGISGE-------VENEPGLMPDGAVIIAAITSCTNTSNPR 417
            +AGPSNPH R+PTS L  RGI+ E        E   GL+PDGAVIIAAITSCTNTSNPR
Sbjct: 361 NMAGPSNPHKRLPTSALHERGIADEDKLAAARAEEAEGLLPDGAVIIAAITSCTNTSNPR 420

Query: 418 NVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACT 477
           NV+AAGLLA+ AN  GL RKPWVKTS APGSK  +LYLEEA LL ELE LGFGIV +ACT
Sbjct: 421 NVVAAGLLAKKANELGLVRKPWVKTSFAPGSKVAKLYLEEAGLLSELEKLGFGIVAYACT 480

Query: 478 TCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 537
           TCNGMSGALDPVIQQE+I+RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG
Sbjct: 481 TCNGMSGALDPVIQQEIIERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 540

Query: 538 TIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYG 597
           T+RFDIE+DVLG DK+G P+ L ++WPSD EIDA++A+SVKPEQF+++Y PMFDL     
Sbjct: 541 TVRFDIEQDVLGTDKNGNPITLKDLWPSDEEIDAIVASSVKPEQFKQIYIPMFDLGT-IE 599

Query: 598 DKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDS 657
           +  SPLYDWRP STYIRRPPYWEGALAGERTLKGMRPLA+L DNITTDHLSPSNAI++DS
Sbjct: 600 EAKSPLYDWRPMSTYIRRPPYWEGALAGERTLKGMRPLAILPDNITTDHLSPSNAILLDS 659

Query: 658 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEP 717
           AAGEYL KMGLPEEDFNSYATHRGDHLTAQRATFANP+L NEMA+VDGK ++GSLAR+EP
Sbjct: 660 AAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPQLVNEMAVVDGKAQKGSLARVEP 719

Query: 718 EGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHR 777
           EG V RMWEAIETYM+RKQ LII+AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHR
Sbjct: 720 EGKVMRMWEAIETYMNRKQNLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 779

Query: 778 TNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTC 837
           TNLVGMGVLP+EFK G  R T G+DGTE FD+ G ++PR DLT++I   +GE   VPVTC
Sbjct: 780 TNLVGMGVLPVEFKPGTTRLTLGLDGTETFDIEGELSPRCDLTLVIHHMSGEETRVPVTC 839

Query: 838 RLDTAEEVSIYEAGGVLQRFAQDFL 862
           RLDTA EVS+Y+AGGVLQRFA+DFL
Sbjct: 840 RLDTAAEVSVYQAGGVLQRFAKDFL 864


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: 2240
Number of extensions: 80
Number of successful extensions: 3
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: 867
Length adjustment: 42
Effective length of query: 825
Effective length of database: 825
Effective search space:   680625
Effective search space used:   680625
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