Alignments for a candidate for acn in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Burkholderia phytofirmans PsJN

Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate BPHYT_RS10160 BPHYT_RS10160 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>FitnessBrowser__BFirm:BPHYT_RS10160
          Length = 861

 Score = 1270 bits (3286), Expect = 0.0
 Identities = 632/862 (73%), Positives = 724/862 (83%), Gaps = 6/862 (0%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           MLE +R H A RA  GI P PL A Q A LVELL  PP GEE+ LLDL+ NRVP GVDEA
Sbjct: 1   MLENFRAHAAARATLGIPPLPLTAQQTAELVELLTNPPAGEEQTLLDLITNRVPAGVDEA 60

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A VKAGFLAAVAKG+TT  L+S  +A ELLGTM GGYNI PLI+ L DA++  +AA+AL 
Sbjct: 61  ARVKAGFLAAVAKGETTCALISRARATELLGTMLGGYNIQPLIELLSDAEVGTVAAEALK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
            TLLMFD F+DV+E A  GN  AK V+QSWADAEWF SRP + + +T+TVFKVTGETNTD
Sbjct: 121 KTLLMFDAFHDVKELADKGNANAKAVLQSWADAEWFTSRPEVPQSLTITVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
           DLSPAPDA +RPDIP+HA AMLKNAR GI P++ G  GPIK I++L++KG+ +AYVGDVV
Sbjct: 181 DLSPAPDATTRPDIPMHALAMLKNARPGITPEEDGKRGPIKFIQSLKEKGHLVAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF G+DIP +PNKR GG+CLG KIAPIF+NTMEDAGALPIE+DVS 
Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDVSQ 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           + MGDV+++ PY+G+   +  G ++A F++K+DVL DEVRAGGRIPLIIGRGLT KAREA
Sbjct: 301 MEMGDVVELRPYEGKALKN--GAVIAEFKVKSDVLFDEVRAGGRIPLIIGRGLTAKAREA 358

Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LGL  S +FR  +  A+S +GFSLAQKMVGRACG+   +G+RPG YCEPKMTSVGSQDTT
Sbjct: 359 LGLAPSTLFRLPQQPADSGKGFSLAQKMVGRACGLPEGQGVRPGTYCEPKMTSVGSQDTT 418

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSADLVMQSFCHTAAYPK VDV TH TLPDFI NRGG++LRPGDG
Sbjct: 419 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKSVDVKTHRTLPDFISNRGGIALRPGDG 478

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATG MPLDMPESVLVRFK
Sbjct: 479 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGTMPLDMPESVLVRFK 538

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           GKMQPG+TLRDLV+AIPLYAIKQG LTV K+GKKNIFSGR+LEIEGLPDLKVEQAFEL+D
Sbjct: 539 GKMQPGVTLRDLVNAIPLYAIKQGTLTVAKQGKKNIFSGRVLEIEGLPDLKVEQAFELSD 598

Query: 598 ASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQL 657
           ASAERSAAGCT+ LNKEPI+EYL SN+ LLKWMIA+GY D R+L+RRI+ ME WLADPQL
Sbjct: 599 ASAERSAAGCTVHLNKEPIIEYLNSNVTLLKWMIAQGYQDPRSLQRRIKAMEAWLADPQL 658

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHF 717
           L  DADAEYAAVI+IDLADI EPI+  PNDPDD + LSDV G KIDEVFIGSCMTNIGHF
Sbjct: 659 LSPDADAEYAAVIEIDLADIHEPIVACPNDPDDVKTLSDVAGAKIDEVFIGSCMTNIGHF 718

Query: 718 RAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAA KLL+  K  +P +LWVAPPT+MD  QLTEEG+Y VFG +GAR E+PGCSLCMGNQA
Sbjct: 719 RAASKLLEG-KRDIPVKLWVAPPTKMDQKQLTEEGHYGVFGTAGARTEMPGCSLCMGNQA 777

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           +V +GATV+STSTRNFPNRLG   NV+L SAELAA+ + +GK+PT EEY   +  +  + 
Sbjct: 778 QVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGKIPTKEEYMADMGVLTASG 837

Query: 838 VDTYRYLNFDQLSQYTEKADGV 859
              Y+Y+NFDQ+  + + AD V
Sbjct: 838 DKIYQYMNFDQIEDFKDLADTV 859


Lambda     K      H
   0.317    0.136    0.400 

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: 2048
Number of extensions: 75
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: 865
Length of database: 861
Length adjustment: 42
Effective length of query: 823
Effective length of database: 819
Effective search space:   674037
Effective search space used:   674037
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