Alignments for a candidate for acn in Actinomyces timonensis 7400942

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Actinomyces timonensis 7400942

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_017178478.1 A1QA_RS0108460 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_000295095.1:WP_017178478.1
          Length = 890

 Score = 1053 bits (2724), Expect = 0.0
 Identities = 536/906 (59%), Positives = 662/906 (73%), Gaps = 33/906 (3%)

Query: 3   NSFQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDI 62
           ++F +  TL      Y YY L          + RLP+S++V+ E+LLR EDG  VT + +
Sbjct: 5   DTFGSRATLDVDGAAYEYYRLN-----AAPGLERLPYSLKVLAENLLRTEDGANVTADHV 59

Query: 63  EALARWRP--DPGEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVP 120
            ALA W P  +P +  +    ARV++QDFTGVP +VDLA MR+A+   GGDP+ INP+ P
Sbjct: 60  RALAAWDPAAEP-DTEIQFTPARVVMQDFTGVPCIVDLATMREAVAELGGDPEVINPLAP 118

Query: 121 ADLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQ 180
           A++VIDHSVQ+D+FG   +   N E+EYERN ERY  L+W Q AL NFRVVPPGTGIVHQ
Sbjct: 119 AEMVIDHSVQIDSFGLPGSLERNKEREYERNAERYQFLRWGQGALSNFRVVPPGTGIVHQ 178

Query: 181 VNIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPY 240
           VNIEYL ++V T + DG+T A+PD+ VGTDSHTTMVNGLGVLGWGVGGIEAEA MLGQP 
Sbjct: 179 VNIEYLARIVFTHEADGVTRAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPV 238

Query: 241 YMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRAT 300
            ML P+VVGFKL G +P GATATD+VLT+TEMLR HGVVGKFVEFYG GVA++   +RAT
Sbjct: 239 SMLIPKVVGFKLSGAIPAGATATDVVLTITEMLRAHGVVGKFVEFYGEGVAEVPLANRAT 298

Query: 301 IANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYS 360
           I NM+PE+G+T   FP+DE TL+YLR TGR EE V LVEAYTKA G++  P A E V YS
Sbjct: 299 IGNMSPEFGSTAAIFPIDEITLDYLRLTGRSEERVRLVEAYTKAQGMWHDP-AREPV-YS 356

Query: 361 EYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFL----AHLTKPVKERGFGLSEDQLQRK 416
           EYLELDLS V PS+AGPKRPQDR+ L   K+SF      + ++P K     L++      
Sbjct: 357 EYLELDLSTVVPSIAGPKRPQDRIVLSRAKESFQEVLPTYASQPSKPTPVTLADGTAT-- 414

Query: 417 VLVKRRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLA 476
                     +L HG V IA+ITSCTNTSNPSVM+ AGLLA+ AV  GL  KPWVKTS A
Sbjct: 415 ----------DLDHGHVAIASITSCTNTSNPSVMMAAGLLARNAVARGLRSKPWVKTSTA 464

Query: 477 PGSKVVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVL 536
           PGS+VVTDY E +GL P L  LGF++VGYGC TCIGNSGPLP ++++AV + +L V +VL
Sbjct: 465 PGSQVVTDYYEKAGLWPALNELGFNVVGYGCATCIGNSGPLPAEVSQAVNDADLAVVSVL 524

Query: 537 SGNRNFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPS 596
           SGNRNFEGRINP VK NYLASP LV+AYALAG MDIDF TEPLG DP G+ ++L DIWP 
Sbjct: 525 SGNRNFEGRINPDVKMNYLASPPLVIAYALAGTMDIDFATEPLGQDPEGRDVFLSDIWPD 584

Query: 597 MEEIREAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDL 656
             E++  I  T+D E++ ++Y+ VF GDERWQ L  P G+ + WD +STY++  PFFE L
Sbjct: 585 PTEVQAVIDSTIDREMYTRDYADVFAGDERWQGLDTPEGDTFAWDKDSTYVRKAPFFEGL 644

Query: 657 GER--KVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSR 714
                 V DI  ARVL +LGDSVTTDHISPAGAI   SPAG+YL   GV   DFNSYGSR
Sbjct: 645 SMELTPVADIEDARVLALLGDSVTTDHISPAGAIKADSPAGRYLAEHGVARADFNSYGSR 704

Query: 715 RGNHEVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAG 774
           RGNHEVM+RGTFANIR++N +LDG+EGGY +    G+ + +++ +  Y+A G PL+V+ G
Sbjct: 705 RGNHEVMIRGTFANIRLRNRLLDGVEGGYTRNFLTGEQESIFDASQAYQAAGIPLVVLGG 764

Query: 775 KEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTG 834
           KEYG+GSSRDWAAKGT LLG++AV+AESFERIHRSNL+GMGV+PL+F  GE+ E+LGL G
Sbjct: 765 KEYGSGSSRDWAAKGTALLGVKAVIAESFERIHRSNLIGMGVVPLQFPAGESAESLGLDG 824

Query: 835 YEVYDILGL----EDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTV 890
            E + I GL    E   PR  V + A++ DGS V F A+ R+DTP E DY+++GGILQ V
Sbjct: 825 TETFSITGLTALNEGTTPR-TVAVTAQKADGSAVSFDAVVRIDTPGEADYFRHGGILQYV 883

Query: 891 LLNMLK 896
           L ++ +
Sbjct: 884 LRSLAR 889


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: 2095
Number of extensions: 97
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: 890
Length adjustment: 43
Effective length of query: 859
Effective length of database: 847
Effective search space:   727573
Effective search space used:   727573
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 2024 update 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