Alignments for a candidate for acn in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Paraburkholderia phymatum STM815

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 WP_041765781.1 BPHY_RS33395 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= SwissProt::Q937N8
         (869 letters)



>NCBI__GCF_000020045.1:WP_041765781.1
          Length = 865

 Score = 1582 bits (4096), Expect = 0.0
 Identities = 791/870 (90%), Positives = 828/870 (95%), Gaps = 6/870 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+A RKPLPGT LDYFD RAAV+AIQPGAYDKLPYTSRV AENLVRRCDPATL DSL Q
Sbjct: 1   MNTAYRKPLPGTSLDYFDTRAAVDAIQPGAYDKLPYTSRVHAENLVRRCDPATLNDSLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           +V RKR+LDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH
Sbjct: 61  IVERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDPDAFAKNRAIEDRRNEDRF FI+WTK+AFKNVDVIPPGNGIMHQINLE+M
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFDFINWTKKAFKNVDVIPPGNGIMHQINLERM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVIHA +GVAYPDT VGTDSHTPHVDALGVIA+GVGGLEAENVMLGRASWMRLPDIVGV
Sbjct: 181 SPVIHAADGVAYPDTLVGTDSHTPHVDALGVIAVGVGGLEAENVMLGRASWMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           EL+GKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA
Sbjct: 241 ELSGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMFFIDEQTIDYLRLTGR D Q+KLVETYA+TAGLWAD+LK+AEYER+L FDLS+VVR
Sbjct: 301 TAAMFFIDEQTIDYLRLTGRDDAQVKLVETYAKTAGLWADTLKHAEYERILSFDLSTVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           NMAGPSNPH+RLPTS LAERGIA        +E  G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHRRLPTSDLAERGIA-----GKWEEVPGQMPDGAVIIAAITSCTNTSNPRNV 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAAALLARNANARGL RKPWVKSSLAPGSKAVELYL+EANLLP+LEKLGFGIVAFACTTC
Sbjct: 416 IAAALLARNANARGLTRKPWVKSSLAPGSKAVELYLQEANLLPELEKLGFGIVAFACTTC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQQEI+DRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPAIQQEIVDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIE+DVLGTD+DGKPVYLKDIWPSDEEIDAIV +SVKPEQFRKVYEPMFA+TAASGE 
Sbjct: 536 RFDIERDVLGTDRDGKPVYLKDIWPSDEEIDAIVKQSVKPEQFRKVYEPMFAVTAASGEP 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           +SPLYDWR QSTYIRRPPYWEGALAGERTLK +RPLAVLGDNITTDHLSPSNAI+ NSAA
Sbjct: 596 ISPLYDWRAQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILANSAA 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
           GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQ+KKGSLARIEPEG
Sbjct: 656 GEYLTKMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQLKKGSLARIEPEG 715

Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
           KV RMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTN
Sbjct: 716 KVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 775

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           LIGMGVLPLEFK GVNRL LG+DGTETYDVIGER+PRA LTLV++RKNGERV+VPVTCRL
Sbjct: 776 LIGMGVLPLEFKRGVNRLALGIDGTETYDVIGERRPRADLTLVIHRKNGERVDVPVTCRL 835

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
           D+ EEVSIYEAGGVL  FAQDFLESS+A A
Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESSKAAA 865


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: 2314
Number of extensions: 93
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: 869
Length of database: 865
Length adjustment: 42
Effective length of query: 827
Effective length of database: 823
Effective search space:   680621
Effective search space used:   680621
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