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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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:

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:

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:

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:

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