Alignments for a candidate for acn in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Trichormus variabilis ATCC 29413

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_011317443.1 AVA_RS02880 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_000204075.1:WP_011317443.1
          Length = 876

 Score = 1140 bits (2948), Expect = 0.0
 Identities = 587/876 (67%), Positives = 688/876 (78%), Gaps = 34/876 (3%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YR+HVAERAA GI P PLDA Q + L ELLKNPP GEE+ LL LL +RV PGVD A
Sbjct: 1   MLESYRQHVAERAALGIPPLPLDAKQTSELCELLKNPPKGEEDTLLHLLRDRVSPGVDPA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAK---------- 110
           AYVKAGFL AIAK E KSP+++   A++LLGTM GGYN+  LI+ L  A           
Sbjct: 61  AYVKAGFLTAIAKQEVKSPIISSIDAVQLLGTMVGGYNVQSLIELLQFATVSVSDSSETP 120

Query: 111 ----------LAPIAAKALSHTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRP 160
                     +A  AA ALS TLL++D F+D+ E AK  N YAK+V+ SWA AEWF +RP
Sbjct: 121 LVMGGEGKEPIAAYAAAALSKTLLVYDAFHDIVELAKT-NPYAKRVVDSWAAAEWFTSRP 179

Query: 161 ALAEKLTVTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPI 220
            L E + VTVFKV GETNTDDLSPA  A +RPDIPLHALAML       E  QPG    +
Sbjct: 180 QLPEYINVTVFKVPGETNTDDLSPATHATTRPDIPLHALAML-------ESRQPG---SL 229

Query: 221 KQIEALQQKGFPLAYVGDVVGTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAP 280
           + I  L++KG P+AYVGDVVGTGSSRKSA NSVLW  G+DIP VPNKR GG  LGG IAP
Sbjct: 230 ETITELKKKGHPVAYVGDVVGTGSSRKSAINSVLWHTGEDIPFVPNKRAGGYILGGAIAP 289

Query: 281 IFFNTMEDAGALPIEVDVSNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVR 340
           IFFNT EDAGALPI+ DV+ L  G VI +YPYKGE+ N E GE+++TF LK D ++DEVR
Sbjct: 290 IFFNTAEDAGALPIQCDVTKLETGMVITIYPYKGEITN-EDGEVISTFTLKPDTILDEVR 348

Query: 341 AGGRIPLIIGRGLTTKAREALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRP 400
           AGGRIPL+IGR LT K R+ALGL  S +F + +  A++ +G++LAQKMVG+ACG+ G+RP
Sbjct: 349 AGGRIPLLIGRTLTDKTRQALGLEPSTLFIRPQPPADTGKGYTLAQKMVGKACGLPGVRP 408

Query: 401 GAYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTL 460
           G  CEP MT+VGSQDTTGPMTRDELK+LACLGFSADLV+Q+FCHTAAYPKPVD+ THH L
Sbjct: 409 GTSCEPIMTTVGSQDTTGPMTRDELKELACLGFSADLVLQTFCHTAAYPKPVDIKTHHEL 468

Query: 461 PDFIMNRGGVSLRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAA 520
           PDF  +R GV+LRPGDG+IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFA A
Sbjct: 469 PDFFSSRAGVALRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPLGISFPAGSGLVAFAGA 528

Query: 521 TGVMPLDMPESVLVRFKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILE 580
            GVMPLDMPESVLVRFKG++QPGITLRD+V+AIP  AI+QGLLTVEK+ KKNIFSGRI+E
Sbjct: 529 LGVMPLDMPESVLVRFKGELQPGITLRDIVNAIPYVAIQQGLLTVEKENKKNIFSGRIME 588

Query: 581 IEGLPDLKVEQAFELTDASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRT 640
           IEGLPDLKVEQAFELTDA+AERS AG TIKL+ E + EYL SN+ LLK MIA GY D RT
Sbjct: 589 IEGLPDLKVEQAFELTDATAERSCAGSTIKLSVETVAEYLRSNVALLKNMIARGYQDSRT 648

Query: 641 LERRIQGMEKWLANPELLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGE 700
           L RRI  ME+WLANP LLE DADAEYAA+I+IDL DIKEPI+ APNDPD+ + LS V  +
Sbjct: 649 LLRRIAKMEEWLANPVLLEGDADAEYAAIIEIDLNDIKEPIVAAPNDPDNVKLLSEVAND 708

Query: 701 KIDEVFIGSCMTNIGHFRAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKS 760
            + EVF+GSCMTNIGH+RA  K+L+   G++ TRLW+APPTRMD  QL EEG YS+FG +
Sbjct: 709 PVQEVFLGSCMTNIGHYRATAKVLEG-AGEVKTRLWIAPPTRMDEHQLKEEGVYSIFGAA 767

Query: 761 GARIEIPGCSLCMGNQARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKL 820
           GAR E+PGCSLCMGNQARVADG TV STSTRNF NR+G GA V+L SAELAAV AL+G++
Sbjct: 768 GARTEMPGCSLCMGNQARVADGTTVFSTSTRNFNNRMGKGARVYLGSAELAAVCALLGRI 827

Query: 821 PTPEEYQTYVA-QVDKTAVDTYRYLNFNQLSQYTEK 855
           PT +EY   VA ++   A + YRYLNF+Q+  + ++
Sbjct: 828 PTVQEYLDIVASKIHPFADNLYRYLNFDQIVGFEDE 863


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: 1959
Number of extensions: 80
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: 865
Length of database: 876
Length adjustment: 42
Effective length of query: 823
Effective length of database: 834
Effective search space:   686382
Effective search space used:   686382
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 24 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

Related tools

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