Alignments for a candidate for acn in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas putida KT2440

Align Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate PP_2336 PP_2336 aconitate hydratase 1

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__Putida:PP_2336
          Length = 862

 Score = 1459 bits (3777), Expect = 0.0
 Identities = 739/867 (85%), Positives = 782/867 (90%), Gaps = 8/867 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+A RK LPGT LDYFDARAAVEAI+PGAYD LPYTSRVLAENLVRRCDPATL  SL Q
Sbjct: 1   MNTAYRKHLPGTDLDYFDARAAVEAIKPGAYDGLPYTSRVLAENLVRRCDPATLDASLSQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           L+ RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIAD+GGDPA+VNPVVPVQLIVDH
Sbjct: 61  LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDP AF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVI PGNGIMHQINLEKM
Sbjct: 121 SLAVECGGFDPQAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIQPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPV+H+D GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP+IVGV
Sbjct: 181 SPVVHSDRGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPEIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK  P ITATD+VLALTEFLRK+KVVGAYLEF GEGA +LTLGDRATISNMAPEYGA
Sbjct: 241 ELTGKLAPNITATDLVLALTEFLRKQKVVGAYLEFHGEGARALTLGDRATISNMAPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF ID+QTIDYLRLTGR ++Q+KLVETYA+  GLWADSL  A YER L FDLSSVVR
Sbjct: 301 TAAMFAIDQQTIDYLRLTGREEQQVKLVETYAKATGLWADSLGGAVYERTLSFDLSSVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           NMAGPSNPH R+ TS LA +GIA      S +E  G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARVATSDLAAKGIA-----GSWEEVPGQMPDGAVIIAAITSCTNTSNPRNV 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA L+ARNAN  GL RKPWVKSSLAPGSKAV+LYLEEA L  +LE+LGFGIVAFACTTC
Sbjct: 416 IAAGLIARNANKLGLTRKPWVKSSLAPGSKAVQLYLEEAGLEKELEQLGFGIVAFACTTC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG   DGK + LKDIWPSDEEIDA+V  +VKPEQFRKVY PMFAI    G  
Sbjct: 536 RFDIEKDVLGV-VDGKEIRLKDIWPSDEEIDAVVRAAVKPEQFRKVYIPMFAIEEDRGPK 594

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           V+PLYDWRP STYIRRPPYWEGALAGERTL+ +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 595 VAPLYDWRPMSTYIRRPPYWEGALAGERTLRGMRPLAVLPDNITTDHLSPSNAIMLDSAA 654

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMA-VVDGQVKKGSLARIEPE 719
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM    DG VK+GSLARIEPE
Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRNDDGSVKQGSLARIEPE 714

Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
           GKV RMWEAIETYM RKQPLII+AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRT
Sbjct: 715 GKVTRMWEAIETYMQRKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 774

Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
           NL+GMGVLPLEFKPG +R TLGLDG+ETYDV+G R PRATLTLVV R NGE +EVPVTCR
Sbjct: 775 NLVGMGVLPLEFKPGTDRKTLGLDGSETYDVLGARTPRATLTLVVTRANGECLEVPVTCR 834

Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESS 865
           LD+ EEVSIYEAGGVL  FAQDFLE++
Sbjct: 835 LDTAEEVSIYEAGGVLQRFAQDFLEAT 861


Lambda     K      H
   0.318    0.135    0.398 

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: 88
Number of successful extensions: 4
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: 869
Length of database: 862
Length adjustment: 42
Effective length of query: 827
Effective length of database: 820
Effective search space:   678140
Effective search space used:   678140
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
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