GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pontibacillus litoralis JSM 072002

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_036833329.1 N784_RS06120 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_000775615.1:WP_036833329.1
          Length = 904

 Score = 1060 bits (2740), Expect = 0.0
 Identities = 544/901 (60%), Positives = 673/901 (74%), Gaps = 6/901 (0%)

Query: 1   MKNSFQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTRE 60
           +K++FQ  K        Y YY L+ LE  G+ ++SRLP+SIRV+LES+LR  DG  + +E
Sbjct: 3   VKDTFQAHKQFELNGKKYNYYKLKTLEEAGLGKISRLPYSIRVLLESVLRQHDGEVIQKE 62

Query: 61  DIEALARWRPDPGE-INVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVV 119
            IE LA+W     E ++VP K +RVILQDFTGVPAVVDLA++R A+   GG P +INP V
Sbjct: 63  HIEKLAKWGSKEAESVDVPFKPSRVILQDFTGVPAVVDLASLRKAMVDMGGSPDKINPEV 122

Query: 120 PADLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVH 179
           P DLVIDHSVQVD +GTA A   N+E E+ERN+ERY  L WA+ A +N++ VPP TGIVH
Sbjct: 123 PVDLVIDHSVQVDEYGTAKALDANMELEFERNKERYEFLNWAKKAFDNYQAVPPATGIVH 182

Query: 180 QVNIEYLTKVVMTGKRD-GLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQ 238
           QVN+EYL  VV   + + G   A+PD+LVGTDSHTTM+NGLGVLGWGVGGIEAEA MLGQ
Sbjct: 183 QVNLEYLANVVHAIENEKGEYDAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAGMLGQ 242

Query: 239 PYYMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDR 298
           P Y  AP V+G KL G LP+G TATDL L VT+ LR+  VVGKFVEF+GPG+ ++   DR
Sbjct: 243 PSYFPAPEVIGVKLTGTLPKGTTATDLALKVTQKLREKNVVGKFVEFFGPGLTEMPLADR 302

Query: 299 ATIANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQ 358
           ATI+NMAPEYGAT GFFPVD+E+L YLR TGR EE ++LVEAY K   LF TP+ E+   
Sbjct: 303 ATISNMAPEYGATCGFFPVDQESLEYLRLTGRSEEQIQLVEAYCKENDLFYTPDQEDPT- 361

Query: 359 YSEYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVL 418
           +++ +E+ L  +EP+L+GPKRPQD +PL E+K+SF   LT P   +GFGL E +  +KV 
Sbjct: 362 FTDLVEIKLDELEPNLSGPKRPQDLIPLTEMKESFNKALTAPEGNQGFGLDEKEKDKKVS 421

Query: 419 VKRRD-EEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAP 477
           V+    +   +  G+V IAAITSCTNTSNP VMLGAGLLAKKAVE GL+   +VKTSLAP
Sbjct: 422 VQHPSGKSSTMKTGAVAIAAITSCTNTSNPYVMLGAGLLAKKAVEKGLEVPEYVKTSLAP 481

Query: 478 GSKVVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLS 537
           GSKVVT YLE SGLM +LE LGF+ VGYGCTTCIGNSGPL  ++ +A+ + +L V++VLS
Sbjct: 482 GSKVVTRYLEDSGLMTYLEKLGFNTVGYGCTTCIGNSGPLSPEVEQAIADNDLTVSSVLS 541

Query: 538 GNRNFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSM 597
           GNRNFEGRI+P VKANYLASP LVVAYALAG +DID   E LG D +GK ++  DIWPSM
Sbjct: 542 GNRNFEGRIHPLVKANYLASPPLVVAYALAGTVDIDLRKESLGKDHDGKDVHFDDIWPSM 601

Query: 598 EEIREAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLG 657
           +EI+  + K ++PE+F+KEY  VF+ +E+W  +      LY WD ESTYIQNPPFF  L 
Sbjct: 602 DEIKAEVDKHVNPEIFRKEYEDVFDSNEKWNQIQTTDEPLYNWDDESTYIQNPPFFVGLS 661

Query: 658 E--RKVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRR 715
           E   +V+D+ G RV+   GDSVTTDHISPAGAI    PAG+YL  KGV P  FNSYGSRR
Sbjct: 662 EDPSEVKDLDGLRVIGKFGDSVTTDHISPAGAIAKDMPAGKYLQDKGVSPRHFNSYGSRR 721

Query: 716 GNHEVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGK 775
           GNHEVMMRGTFANIRI+N +  G EGGY    P  +V  +Y+ AM+Y+ +GT LLVIAG 
Sbjct: 722 GNHEVMMRGTFANIRIRNKIAPGTEGGYTTFWPTDEVMPIYDAAMKYQEQGTGLLVIAGN 781

Query: 776 EYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGY 835
           +YG GSSRDWAAKGT LLGI+ V+AESFERIHRSNLV MGVLPL+F  G++ ++LGL+G 
Sbjct: 782 DYGMGSSRDWAAKGTNLLGIKTVIAESFERIHRSNLVMMGVLPLQFKDGDSADSLGLSGK 841

Query: 836 EVYDILGLEDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNML 895
           E +DI   E +KPR LVD++A  E G++  FQ IAR D+ VE+DYY++GGILQ VL + L
Sbjct: 842 ETFDIKIDETVKPRDLVDVIAIDEAGNKTEFQVIARFDSGVEIDYYRHGGILQKVLRDKL 901

Query: 896 K 896
           +
Sbjct: 902 Q 902


Lambda     K      H
   0.317    0.137    0.399 

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: 2257
Number of extensions: 104
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: 902
Length of database: 904
Length adjustment: 43
Effective length of query: 859
Effective length of database: 861
Effective search space:   739599
Effective search space used:   739599
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 24 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