Alignments for a candidate for acn in Amantichitinum ursilacus IGB-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Amantichitinum ursilacus IGB-41

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_053935982.1 WG78_RS01355 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_001294205.1:WP_053935982.1
          Length = 897

 Score = 1000 bits (2586), Expect = 0.0
 Identities = 515/899 (57%), Positives = 654/899 (72%), Gaps = 20/899 (2%)

Query: 7   TLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDIEALA 66
           TLKTL   +    YY L  LE  G+  +SRLP SIR++LES+LRN DG +VT E +  LA
Sbjct: 8   TLKTLPDTAPALQYYSLPALEAAGIGPISRLPVSIRLVLESVLRNCDGKKVTEEHVRQLA 67

Query: 67  RWRPDPGEIN-VPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPADLVI 125
            W+P    ++ +P  +ARV+LQDFTGVP + DLAAMR+     G +PK I P+VP DLV+
Sbjct: 68  NWKPTGHRVDEIPFVVARVVLQDFTGVPLLADLAAMRNVADKLGKNPKLIEPLVPVDLVV 127

Query: 126 DHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVNIEY 185
           DHSVQVD +GT  A   N+E E++RN ERY  +KW   A + F+VVPPG GIVHQVN+EY
Sbjct: 128 DHSVQVDYYGTPDALRKNMEMEFQRNSERYQFMKWGMQAFDTFKVVPPGVGIVHQVNLEY 187

Query: 186 LTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYYMLAP 245
           L + V    RDG+  AFPD+LVGTDSHTTM+N +GV+GWGVGGIEAEA MLGQP Y L P
Sbjct: 188 LFRGVQV--RDGI--AFPDTLVGTDSHTTMINAVGVVGWGVGGIEAEAGMLGQPVYFLTP 243

Query: 246 RVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATIANMA 305
            V+G +L G L EG TATDLVL VTE+LR   VVGKFVEF+GPG A L+  DRATIANMA
Sbjct: 244 DVIGVELSGHLREGVTATDLVLAVTELLRHEKVVGKFVEFFGPGTASLTVTDRATIANMA 303

Query: 306 PEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSEYLEL 365
           PEYGATMGFFPVDE+T+ YL+ TGR +  +   EAY KA  LF  P+A E + Y+  ++L
Sbjct: 304 PEYGATMGFFPVDEKTIAYLQGTGRTDAEIAQFEAYFKAQNLFGIPQAGE-IDYTRVVKL 362

Query: 366 DLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVKRRDEE 425
           DL  + PSLAGPKRPQDR+ L  +K SF +    PV   GF     QL  +    R+   
Sbjct: 363 DLDGIVPSLAGPKRPQDRIALTAMKTSFNSLFAAPVTANGFNKKSSQLAERYPTARQG-- 420

Query: 426 FELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSKVVTDY 485
            ++ +G ++IAAITSCTNTSNP VML +GLLAKKAVE GL  KP +KTSLAPGS+VVT+Y
Sbjct: 421 IDIGNGDILIAAITSCTNTSNPGVMLASGLLAKKAVEKGLSVKPHIKTSLAPGSRVVTEY 480

Query: 486 LEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNRNFEGR 545
           L  +GL+  L  LGF L GYGCTTCIGN+G L  +  +A++  ++V AAVLSGNRNFE R
Sbjct: 481 LTRTGLLEPLAQLGFALAGYGCTTCIGNAGDLAPEFNEAIQLHDVVAAAVLSGNRNFEAR 540

Query: 546 INPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEIREAIR 605
           I+P+++AN+LASP LVVA+A+AGR +ID TTEPLG   +G+P+YL+DIWPS +E+ E ++
Sbjct: 541 IHPNIRANFLASPPLVVAFAIAGRANIDLTTEPLGTGKDGQPVYLRDIWPSSDEVAELLK 600

Query: 606 KTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGER--KVED 663
             LDPE+F+  YS + +  + W  +PAP G++Y W PESTYI  PPFF+        ++D
Sbjct: 601 FALDPEVFRTLYSDLTKDLDLWNNIPAPQGQVYSW-PESTYIARPPFFDQFSPTPGSIDD 659

Query: 664 IRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGNHEVMMR 723
           I+GAR LLVLGDSVTTDHISPAG+   K+PAGQYLI+ GV   DFNSYGSRRGNH+VM+R
Sbjct: 660 IKGARALLVLGDSVTTDHISPAGSFGEKTPAGQYLIAHGVARPDFNSYGSRRGNHDVMIR 719

Query: 724 GTFANIRIKNLML----DG--IEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGKEY 777
           GTFAN+R+KNLML    DG  +EGG+   L +  +  VY+ A  Y   G P +V AG+EY
Sbjct: 720 GTFANVRVKNLMLPAKADGGRVEGGFT--LLDNTLSTVYDAAQAYMERGAPTIVFAGEEY 777

Query: 778 GTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGYEV 837
           GTGSSRDWAAKGT LLG++AV+A+SFERIHRSNLVGMGVLPL+F   ++ ++LG+TG E+
Sbjct: 778 GTGSSRDWAAKGTLLLGVKAVIAKSFERIHRSNLVGMGVLPLQFKGNDSVQSLGITGNEL 837

Query: 838 YDILGL-EDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNML 895
           + +LG+ E LKP++ + +V    DG +     + R+DTP+EVDYYK+GGIL  VL ++L
Sbjct: 838 FAVLGVDEHLKPQQDLTLVICHPDGQKQHIPVLCRIDTPIEVDYYKHGGILPYVLRDLL 896


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: 2230
Number of extensions: 108
Number of successful extensions: 9
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: 897
Length adjustment: 43
Effective length of query: 859
Effective length of database: 854
Effective search space:   733586
Effective search space used:   733586
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