Alignments for a candidate for acn in Synechococcus elongatus PCC 7942

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Synechococcus elongatus PCC 7942

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 Synpcc7942_0903 Synpcc7942_0903 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>FitnessBrowser__SynE:Synpcc7942_0903
          Length = 861

 Score = 1146 bits (2964), Expect = 0.0
 Identities = 580/858 (67%), Positives = 688/858 (80%), Gaps = 16/858 (1%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           MLE YR+  AER A G+ P PLDA Q AAL ELL+ PPVGEE  LL LL +RVPPGVD+A
Sbjct: 1   MLEAYRQAAAEREALGVPPLPLDADQTAALCELLQAPPVGEEATLLHLLRDRVPPGVDQA 60

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALD--DAKLAPIAAKA 118
           AYVKA FL+A+A G+TTSPL+ P +A+ELLGTM GGYN+  LID L   D  +A  A  A
Sbjct: 61  AYVKATFLSAIAHGETTSPLIMPVEAVELLGTMIGGYNVAALIDLLKSADVAIATAAVAA 120

Query: 119 LSHTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETN 178
           LS TLL++D + DV   A+  N YA+QV++SWA AEWF S+P L E ITVT+FKV GETN
Sbjct: 121 LSKTLLVYDAYNDVVALAET-NAYAQQVLESWAKAEWFTSKPTLPEAITVTIFKVPGETN 179

Query: 179 TDDLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGD 238
           TDDLSPA  A +RPDIPLHAQAML+            + G ++ I  L++KGYPLAYVGD
Sbjct: 180 TDDLSPATHATTRPDIPLHAQAMLETR----------LPGSLETIPVLKEKGYPLAYVGD 229

Query: 239 VVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298
           VVGTGSSRKSA NSVLW +G+DIP VPNKR GG+ LGGKIAPIFFNT ED+GALPIE DV
Sbjct: 230 VVGTGSSRKSAINSVLWHIGEDIPFVPNKRSGGIILGGKIAPIFFNTAEDSGALPIECDV 289

Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
           S L+ G V+ +YPY+G +++ E G +L+TF LK D ++DEVRAGGRIPL+IGR LT K R
Sbjct: 290 SALDTGMVVTIYPYEGVIKD-EAGTVLSTFSLKPDTILDEVRAGGRIPLLIGRSLTDKVR 348

Query: 359 EALGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTG 418
             LGLP SDVF + +  A++ +GF+LAQKMVGRACG+ G+RPG  CEP MT+VGSQDTTG
Sbjct: 349 SQLGLPVSDVFVRPQPPADTGKGFTLAQKMVGRACGLPGVRPGTSCEPIMTTVGSQDTTG 408

Query: 419 PMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGV 478
           PMTRDE+K+LACLGFSADLVMQSFCHTAAYPKPVD+ TH TLPDFI  RGGV+L+PGDG+
Sbjct: 409 PMTRDEMKELACLGFSADLVMQSFCHTAAYPKPVDIKTHKTLPDFIAQRGGVALKPGDGI 468

Query: 479 IHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKG 538
           IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAA G MPLDMPESVLVRF G
Sbjct: 469 IHSWLNRMLLPDTVGTGGDSHTRFPLGISFPAGSGLVAFAAAIGAMPLDMPESVLVRFTG 528

Query: 539 KMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDA 598
            +QPGITLRD+V+AIP  AI+QGLLTV K+ K N+FSGRI+EIEGLPDLK+EQAFELTDA
Sbjct: 529 SLQPGITLRDVVNAIPYQAIQQGLLTVSKENKVNVFSGRIMEIEGLPDLKLEQAFELTDA 588

Query: 599 SAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQLL 658
           +AERS AG TIKL+++ + EYL SN+ L+K MIA GY D RTL RRI+ ME WLA+PQLL
Sbjct: 589 TAERSCAGSTIKLSEDTVAEYLRSNVALMKNMIARGYEDSRTLARRIRQMEDWLANPQLL 648

Query: 659 EADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFR 718
            AD DAEYAAVI+I+L ++ EPIL  PNDPD+ + LS+V G+ I E+FIGSCMTNIGH+R
Sbjct: 649 SADEDAEYAAVIEINLDELTEPILACPNDPDNVKKLSEVAGDPIHEIFIGSCMTNIGHYR 708

Query: 719 AAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQAR 778
           AA K+L+  +GQ+  RLW+ PPTRMD  +L EEGYYS F  +GAR+E+PGCSLCMGNQAR
Sbjct: 709 AAAKVLEG-EGQVGGRLWICPPTRMDEDRLKEEGYYSTFAAAGARLEVPGCSLCMGNQAR 767

Query: 779 VADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQ-VDKTA 837
           VAD  TV STSTRNF NR+G GA V+L SAELAAV AL+G++PT EEY    A+ ++  A
Sbjct: 768 VADNTTVFSTSTRNFNNRMGKGAQVYLGSAELAAVCALLGRIPTLEEYLKVAAEKINPFA 827

Query: 838 VDTYRYLNFDQLSQYTEK 855
            D Y+YLNFDQL  + E+
Sbjct: 828 ADLYQYLNFDQLEGFAEE 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: 1908
Number of extensions: 74
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: 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, or view the source code.

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