Alignments for a candidate for acn in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Sedimenticola selenatireducens DSM 17993

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_029132398.1 A3GO_RS0104540 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_000428045.1:WP_029132398.1
          Length = 903

 Score = 1012 bits (2617), Expect = 0.0
 Identities = 534/911 (58%), Positives = 656/911 (72%), Gaps = 33/911 (3%)

Query: 1   MKNSFQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTRE 60
           M  S++   TLT     Y  Y   +L+++   E  RLPFS+R++LE+LLR+     VT E
Sbjct: 1   MSTSYKQAVTLTVGQTDYTIYPFDQLQKRYAIE--RLPFSLRILLENLLRHGSEIFVTDE 58

Query: 61  DIEALARWRP--DPGEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPV 118
           D+E LA W P  +P +  +    +RV+LQDFTGVPA+VDLAAMRDA+   GG P  INP+
Sbjct: 59  DVEFLANWDPQAEPTQ-EIAFVPSRVLLQDFTGVPAIVDLAAMRDAMVELGGSPASINPL 117

Query: 119 VPADLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIV 178
            P +LVIDHSV VD FGTA A   N E E  RN ERY  L+W Q A ENF VVPPGTGIV
Sbjct: 118 SPVELVIDHSVMVDHFGTAEALNQNTEIEISRNLERYKFLRWGQTAFENFSVVPPGTGIV 177

Query: 179 HQVNIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQ 238
           HQVN+EYL + V T + DG  LA+PDSLVGTDSHTTM+NGLGVLGWGVGGIEAEA MLGQ
Sbjct: 178 HQVNLEYLARGVFTKQCDGEQLAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 237

Query: 239 PYYMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDR 298
           P  ML P+VVGF+L G+LPEGATATDLVLTVTE LR+ GVVGKFVEF+G G+A LS  DR
Sbjct: 238 PITMLIPQVVGFRLVGKLPEGATATDLVLTVTERLRQFGVVGKFVEFFGNGLANLSLADR 297

Query: 299 ATIANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFR---TPEAEE 355
           ATIANMAPEYGAT G FP+D ET+ YL+ TGR E  ++LVE+YT+ +GL+    TPEA+ 
Sbjct: 298 ATIANMAPEYGATCGIFPIDAETIRYLQLTGRDEHTLQLVESYTRRMGLWHDADTPEAD- 356

Query: 356 KVQYSEYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFL-------------AHLTKPVK 402
              YS  L LDLS V PS+AGPKRPQDR+PL E K SFL             A +T   +
Sbjct: 357 ---YSALLTLDLSEVVPSIAGPKRPQDRIPLTEAKASFLHLLSEHRQQAPATADVTDFDE 413

Query: 403 ERGFGLSEDQLQRKVLVKRRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVE 462
           E G   S+      V V  R E F L  G+VVIAAITSCTNTSNP+V++ AGLLA+ A +
Sbjct: 414 EGGHPPSD---SGAVEVTYRGETFNLEQGAVVIAAITSCTNTSNPAVLVAAGLLARNARK 470

Query: 463 AGLDRKPWVKTSLAPGSKVVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIA 522
            GL  KPWVKTS APGSKVVTDYL+ +GLM  LEALGF+LVGYGCTTCIGNSGPL ++I+
Sbjct: 471 LGLKAKPWVKTSFAPGSKVVTDYLQRAGLMEELEALGFYLVGYGCTTCIGNSGPLAKEIS 530

Query: 523 KAVEEGNLVVAAVLSGNRNFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFD 582
           + +  GNL+V +VLSGNRNFEGRI+  V+ANYLASP LVVAYALAG M++D   +P+G  
Sbjct: 531 QGINAGNLLVTSVLSGNRNFEGRIHQEVRANYLASPPLVVAYALAGNMNVDLYNDPIGHG 590

Query: 583 PNGKPIYLKDIWPSMEEIREAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDP 642
           P GKP+ L DIWP+  EI++ +  +LD E+F+K+Y  V+ G+E W  LP  TGE Y W  
Sbjct: 591 PEGKPVTLSDIWPASSEIQQVMAGSLDAEMFRKKYQDVYTGNEIWNNLPIETGERYAWS- 649

Query: 643 ESTYIQNPPFFEDLGERK--VEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLIS 700
           +STY++ P FFE + E++  V  I  AR L+ + DS+TTDHISPAGAI V SPAG+YL +
Sbjct: 650 DSTYVRLPTFFERIAEKRPGVNSIEDARCLVKVADSITTDHISPAGAIAVDSPAGRYLQA 709

Query: 701 KGVKPEDFNSYGSRRGNHEVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFVYNVAM 760
             V P+DFNSYGSRRGNHEVMMRGTFANIR++N +  G EG +    P G+   +++ A 
Sbjct: 710 HRVAPQDFNSYGSRRGNHEVMMRGTFANIRLQNQLAPGTEGSWTTHFPSGEQLSIFDAAE 769

Query: 761 RYKAEGTPLLVIAGKEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLE 820
           RYK   TPL+V+AGKEYGTGSSRDWAAKG  LLG++AV+AES+ERIHRSNL+GMG+LPL+
Sbjct: 770 RYKEAQTPLIVLAGKEYGTGSSRDWAAKGPALLGVKAVIAESYERIHRSNLIGMGILPLQ 829

Query: 821 FLPGENRETLGLTGYEVYDILGLEDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDY 880
           F   E+ + L L G E + I  + +   ++ V + ARRE G  + F+A  R+DTP E  Y
Sbjct: 830 FRAEESADVLNLEGTEYFSIPAITE--GQESVVVSARRESGGMISFKAKIRIDTPNEFAY 887

Query: 881 YKNGGILQTVL 891
           Y+NGGIL  VL
Sbjct: 888 YENGGILHFVL 898


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: 2070
Number of extensions: 81
Number of successful extensions: 8
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: 903
Length adjustment: 43
Effective length of query: 859
Effective length of database: 860
Effective search space:   738740
Effective search space used:   738740
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 Apr 09 2024. 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