Alignments for a candidate for acn in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Paraburkholderia bryophila 376MFSha3.1

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate H281DRAFT_06210 H281DRAFT_06210 aconitate hydratase

Query= SwissProt::P37032
         (891 letters)



>FitnessBrowser__Burk376:H281DRAFT_06210
          Length = 898

 Score =  879 bits (2270), Expect = 0.0
 Identities = 448/873 (51%), Positives = 594/873 (68%), Gaps = 24/873 (2%)

Query: 23  YYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTKDIKAIADWLHNKTSQHEIA 82
           Y  LK AE + F  ++ LP SL++LLEN +R          D+ AI DWL  + S  EI+
Sbjct: 23  YADLKRAEAQGFAPLSELPVSLRILLENAMRRGG-----VDDVAAIRDWLTRRESDREIS 77

Query: 83  FRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLSPVDLVIDHSVMVDKFASAD 142
           F P RVLM D + VP V DLAAMR A+ K GG++ +++PL PVD+V+DHS + D    +D
Sbjct: 78  FFPVRVLMPDSSAVPLVADLAAMRDAVRKKGGDSWRVNPLIPVDIVVDHSAITDHAGRSD 137

Query: 143 ALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICHQVNLEYLGKTVWNSENDGQ 202
           A ++N  +E +RN ERY FL+W Q AF N +VVPP TGI HQVNLE+L   V     D  
Sbjct: 138 AFDLNLALEYQRNHERYAFLKWAQNAFDNVRVVPPATGIVHQVNLEFLAAGVQTVVIDDV 197

Query: 203 LYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLSGKLKE 262
            +  PDTLVG DSHTTM+N +GVLGWGVGGIEA AA+LGQP+SML+P VIG ++SG+ + 
Sbjct: 198 TFVVPDTLVGMDSHTTMVNSIGVLGWGVGGIEAAAAILGQPISMLLPRVIGCRISGRPRS 257

Query: 263 GITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADRATISNMAPEYGATCGFFPVD 322
           G+T TD+VL++T+ LR K VVG FVEF+G GL++LP++DRATI+NMAPE GAT  FFP D
Sbjct: 258 GVTCTDIVLSLTEFLRGKKVVGCFVEFFGEGLDNLPVSDRATIANMAPEAGATMCFFPPD 317

Query: 323 KETIKYLELTGRDKHTIALVEAYAKAQGMWYDK---DNEEPVFTDSLHLDLGSVEPSLAG 379
             TI+YL  TGR +  +A+ EA  KAQG+W  +   D E   ++D L  DL +V PS+AG
Sbjct: 318 AATIEYLHATGRSREQVAVAEAVLKAQGIWRPEAGADEERIAYSDRLEFDLSAVTPSMAG 377

Query: 380 PKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDFQMKHGHVVIAAITSCTNTS 439
           PKRPQD+V+L  +   F+             + F +  +   + +G VVIAAITSCTNTS
Sbjct: 378 PKRPQDRVDLKDVSARFH-------------REFGLTAEGRGLTNGSVVIAAITSCTNTS 424

Query: 440 NPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRHAGLQTYLDQLGFNLVGY 499
           N   ++ AGL+A+    +G++ K WVK+SL+PGS+VVTDYLR +GLQ  LD LGFNL GY
Sbjct: 425 NARAMIGAGLIARNLRARGVKPKAWVKTSLSPGSRVVTDYLRESGLQDDLDSLGFNLTGY 484

Query: 500 GCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHPQVRANWLASPPLVVAYA 559
           GC TC G+SG L  +++  +    LVV++VLSGNRNFEGR HP  RAN+L SP LVVAYA
Sbjct: 485 GCMTCAGSSGQLDAEVARRILSEGLVVATVLSGNRNFEGRTHPLARANFLGSPALVVAYA 544

Query: 560 LCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEVAK-VSGTMFRKEYAEVFKGDA 618
             GT   DL+ EPI  + +G  V L D+WP + +I A   + V+ TMF++ YA  F+G+A
Sbjct: 545 CAGTILRDLTTEPIADEADGQPVMLADVWPDDADIDAIFRRIVTLTMFKRVYATAFQGEA 604

Query: 619 HWQAIQTSSGQTYEWNPDSTYIQHPPFFE-NLSLKPEPLKPIKQAYVLALFGDSITTDHI 677
            WQ I  +SG  ++W+  STYI+ PP+F+   +     +  I  A  L + GDSITTDHI
Sbjct: 605 RWQRIAAASGDHFDWDQASTYIRRPPYFDAGFADDGFGMANIVGARALLMLGDSITTDHI 664

Query: 678 SPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTFANIRIRNEMTPGQEGG 737
           SP G I++ + AG +L   GV   DFN+  SRR NH+VMMRGTFAN+R+RNEMTP +EG 
Sbjct: 665 SPVGVIRSETEAGRFLHGAGVAPSDFNTLLSRRANHDVMMRGTFANVRLRNEMTPDREGP 724

Query: 738 VTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWAAKGTNLLGVKAVITES 797
            +R+VP+G+ M ++ AA RY++ +  L++IAG +YG GSSRDWAAKG  LLGV+AVI ES
Sbjct: 725 WSRHVPSGDVMRVFQAASRYRDERVPLIVIAGADYGAGSSRDWAAKGPRLLGVRAVIAES 784

Query: 798 FERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISI-EISDKLTPGAMVPVTIERQDG 856
           FERIHRSNL+GMGILPLQF  GTTRKTL L G E  +I  I   L P   +   + R +G
Sbjct: 785 FERIHRSNLVGMGILPLQFPPGTTRKTLGLTGEESFTIFGIEGALQPHQRIECEVSRANG 844

Query: 857 DIEKIETLCRIDTADELEYYKNGGILQYVLRKI 889
             + I  +CR+D   E+ +Y++GG+LQY+  ++
Sbjct: 845 ARDSITLICRLDIPREIAWYRHGGVLQYIAAQL 877


Lambda     K      H
   0.316    0.134    0.393 

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: 1782
Number of extensions: 70
Number of successful extensions: 7
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: 891
Length of database: 898
Length adjustment: 43
Effective length of query: 848
Effective length of database: 855
Effective search space:   725040
Effective search space used:   725040
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 (21.6 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