Alignments for a candidate for acn in Trichodesmium erythraeum IMS101

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Trichodesmium erythraeum IMS101

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_011610496.1 TERY_RS03160 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_000014265.1:WP_011610496.1
          Length = 869

 Score = 1116 bits (2886), Expect = 0.0
 Identities = 566/859 (65%), Positives = 679/859 (79%), Gaps = 18/859 (2%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE Y   + +RA  GI P PLDA Q + L ELLK+PP G EE L+ LL  RVPPGVDEA
Sbjct: 1   MLENYNNQIQQRATLGIPPLPLDAEQTSDLCELLKSPPIGTEEKLMTLLRLRVPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDAL--DDAKLAPIAAKA 118
           AYVKAGFL  IAKGE  +PL+TP  A+ELLGTM GGYN+  LID L  ++++LA  AA A
Sbjct: 61  AYVKAGFLTGIAKGEITTPLITPTYAVELLGTMVGGYNVQSLIDILKSENSELASTAATA 120

Query: 119 LSHTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETN 178
           LS  LL++D F DV +  +  N YAK+V+ SWA AEWF  RP L E +TVTVFKV GETN
Sbjct: 121 LSKILLVYDAFNDVIKLGET-NPYAKKVVDSWAAAEWFTTRPQLPEAITVTVFKVPGETN 179

Query: 179 TDDLSPAPDAWSRPDIPLHALAMLKNAR-EGIEPDQPGVVGPIKQIEALQQKGFPLAYVG 237
           TDDLSPAP A +RPDIPLHALAML++   EG+           K I  L+QKG P+AYVG
Sbjct: 180 TDDLSPAPHATTRPDIPLHALAMLESKMPEGL-----------KTIAQLKQKGHPVAYVG 228

Query: 238 DVVGTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVD 297
           D+VGTGSSRKSA NS+LW +G+DIP +PNKR GG  LGGKIAPIFFNT ED+GALPIE D
Sbjct: 229 DIVGTGSSRKSACNSMLWHIGEDIPFIPNKRSGGYILGGKIAPIFFNTAEDSGALPIECD 288

Query: 298 VSNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKA 357
           V+ +  G VI +YPYKGE+ N E GE+++TF LK + ++DEVRAGGRIPL+IGR LT K 
Sbjct: 289 VTKMETGMVITIYPYKGEIIN-EAGEIISTFTLKPETMLDEVRAGGRIPLLIGRTLTDKT 347

Query: 358 REALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTT 417
           R  LGL  S VF + +   ++ +GF+LAQKMVG+ACG+ GIRPG  CEP MT+VGSQDTT
Sbjct: 348 RNILGLETSSVFTRPQLPTDTGKGFTLAQKMVGKACGLAGIRPGTACEPLMTTVGSQDTT 407

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDE+K+LACLGFSADLVMQSFCHTAAYPKPVD+NTH  LPDF   RGGV+LRPGDG
Sbjct: 408 GPMTRDEMKELACLGFSADLVMQSFCHTAAYPKPVDINTHKELPDFFSARGGVALRPGDG 467

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           +IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAA G+MPLDMPESVLVRFK
Sbjct: 468 IIHSWLNRMLLPDTVGTGGDSHTRFPLGISFPAGSGLVAFAAALGLMPLDMPESVLVRFK 527

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           G++QPG+TLRD+V+AIP  AI++GLLTV  + KKN+FSGRI+E+EGLP LKVEQAFELTD
Sbjct: 528 GELQPGVTLRDIVNAIPYVAIQKGLLTVALENKKNVFSGRIMEMEGLPYLKVEQAFELTD 587

Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
           A+AERS AG TIKL  E I EYL SN+ LLK M+A GY D RT+ RR+  ME+WLANP+L
Sbjct: 588 ATAERSCAGSTIKLGAETISEYLRSNVTLLKNMVARGYQDTRTIMRRVSKMEQWLANPKL 647

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
           + ADA+AEYA +I++DL +IKEPI+ APNDPD+ + +S   G+KIDEVFIGSCMTNIGH+
Sbjct: 648 MSADANAEYAEIIEVDLNEIKEPIVAAPNDPDNIKLMSECAGDKIDEVFIGSCMTNIGHY 707

Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAA K+L+   G++   LW+ PPTRMD  QL EEG Y VF  +GAR+E+PGCSLCMGNQA
Sbjct: 708 RAAAKVLEG-AGRVKGVLWICPPTRMDEKQLREEGIYGVFAAAGARMEMPGCSLCMGNQA 766

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQ-VDKT 836
           RV +G TV STSTRNF NR+G GA V+L SAELAAV AL+G++P+ +EY   + + VD  
Sbjct: 767 RVKNGVTVFSTSTRNFNNRMGKGARVYLGSAELAAVCALLGRIPSVDEYLDIMKEKVDPF 826

Query: 837 AVDTYRYLNFNQLSQYTEK 855
           A D YRYLNF+Q++ + ++
Sbjct: 827 AGDLYRYLNFDQIAGFEDE 845


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: 1929
Number of extensions: 80
Number of successful extensions: 6
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: 869
Length adjustment: 42
Effective length of query: 823
Effective length of database: 827
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 Sep 24 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