Alignments for a candidate for acn in Laceyella sediminis RHA1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Laceyella sediminis RHA1

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_022736982.1 CLV36_RS07505 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_003003125.1:WP_022736982.1
          Length = 907

 Score = 1109 bits (2869), Expect = 0.0
 Identities = 558/902 (61%), Positives = 683/902 (75%), Gaps = 5/902 (0%)

Query: 5   FQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDIEA 64
           F     L      Y YY L  LE +G+  VSRLPFSI+V+LE+ +R  DG  VT+E IE 
Sbjct: 6   FHVRSKLKVGEQEYVYYRLNGLEEQGIGPVSRLPFSIKVLLEAAVRQYDGKAVTKEHIEQ 65

Query: 65  LARWRPDPGEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPADLV 124
           LA W     +  +  K AR++LQDFTGVPAVVDLAA+R A+   GGDP+RINP++P DLV
Sbjct: 66  LATWADKRSDKEIAFKPARIVLQDFTGVPAVVDLAALRSAMARVGGDPERINPLIPVDLV 125

Query: 125 IDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVNIE 184
           IDHSV VD  GT  A  YN+  E+ERN ERY LL+WA  +L+NFR VPP TGIVHQVN+E
Sbjct: 126 IDHSVMVDKAGTQDALEYNMNLEFERNEERYRLLRWAAESLDNFRAVPPATGIVHQVNLE 185

Query: 185 YLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYYMLA 244
           YL  V  T + DG T+ FPDSLVGTDSHTTM+NGLGV+GWGVGGIEAEA MLGQP Y + 
Sbjct: 186 YLANVAATREVDGETVVFPDSLVGTDSHTTMINGLGVVGWGVGGIEAEACMLGQPLYFIT 245

Query: 245 PRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATIANM 304
           P V+GFKL G+LP+GATATDL LTVTEMLRK GVVGKFVEFYGPG++ LS  DRAT+ANM
Sbjct: 246 PEVIGFKLTGQLPDGATATDLALTVTEMLRKKGVVGKFVEFYGPGLSNLSLADRATVANM 305

Query: 305 APEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSEYLE 364
           APEYGAT+GFFPVD+E LNYLR TGR EELV LV+ Y +A GLFRT +  + V +++ +E
Sbjct: 306 APEYGATIGFFPVDDEALNYLRNTGRDEELVTLVKEYYQAQGLFRTDDTPDPV-FTDTVE 364

Query: 365 LDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVKRRD- 423
           LDLS V PSL+GPKRPQDR+ L  +K+++   L KP+ +RGFGLSE++  +   V   D 
Sbjct: 365 LDLSTVVPSLSGPKRPQDRIELTAMKEAWNETLRKPIDQRGFGLSEEECAKSAQVSLPDG 424

Query: 424 EEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSKVVT 483
             ++L  G+VVIAAITSCTNTSNPSVM+GAGL+AKKAVE GL  KP+VK+SL PGSKVVT
Sbjct: 425 STYQLDQGAVVIAAITSCTNTSNPSVMVGAGLVAKKAVEKGLTVKPFVKSSLTPGSKVVT 484

Query: 484 DYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNRNFE 543
           DYL+ +GL+  L  LGF + GYGC TCIGNSGPL ++++KA+EE +L VA+VLSGNRNFE
Sbjct: 485 DYLDKAGLIEPLAKLGFTVAGYGCATCIGNSGPLSDEVSKAIEENDLTVASVLSGNRNFE 544

Query: 544 GRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEIREA 603
           GRI+P VKANYLASP LVVAYALAG ++IDF TEP+G +  G+ IYLKDIWPS  EI + 
Sbjct: 545 GRIHPLVKANYLASPPLVVAYALAGTVNIDFATEPIGHNDAGEAIYLKDIWPSSHEISQV 604

Query: 604 IRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGE--RKV 661
           +   +  E F+K+Y++VF+ +ERW  LP P G LY+WD +STYIQ PPFF D+     ++
Sbjct: 605 MNSAISAEQFRKQYAQVFDANERWNQLPTPKGVLYEWDQDSTYIQEPPFFVDMSADVEEI 664

Query: 662 EDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGNHEVM 721
           + I GA +L +L DSVTTDHISPAG+I   SPAG+YL  KGV  +DFNSYGSRRGN  VM
Sbjct: 665 KPITGAHILALLNDSVTTDHISPAGSIAPTSPAGRYLQDKGVAIKDFNSYGSRRGNDRVM 724

Query: 722 MRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGKEYGTGS 781
            RGTFANIRI+N M+ G EGG  K +P   V  +Y+ AM YK  GTPL+VIAGKEYGTGS
Sbjct: 725 TRGTFANIRIRNQMVPGSEGGVTKHVPSQQVMSIYDAAMEYKKSGTPLVVIAGKEYGTGS 784

Query: 782 SRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGYEVYDIL 841
           SRDWAAKGT LLG++AV+AESFERIHRSNLVGMGVLPL+F  G N ++LGL G E  DI 
Sbjct: 785 SRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFANGANWQSLGLDGTEKIDIA 844

Query: 842 GLED-LKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNMLKEAKA 900
           GL D + P + + + A + DGS V+F    RLD+ V+++YY+NGGILQTVL  +L   + 
Sbjct: 845 GLNDEVTPGQTLTVTATKPDGSSVQFDVTVRLDSVVDIEYYRNGGILQTVLRQILANQEG 904

Query: 901 TE 902
           ++
Sbjct: 905 SK 906


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: 2153
Number of extensions: 84
Number of successful extensions: 5
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: 907
Length adjustment: 43
Effective length of query: 859
Effective length of database: 864
Effective search space:   742176
Effective search space used:   742176
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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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