Alignments for a candidate for acn in Herbaspirillum autotrophicum IAM 14942

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Herbaspirillum autotrophicum IAM 14942

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_050461996.1 AKL27_RS06545 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_001189915.1:WP_050461996.1
          Length = 897

 Score =  956 bits (2470), Expect = 0.0
 Identities = 490/902 (54%), Positives = 637/902 (70%), Gaps = 17/902 (1%)

Query: 2   KNSFQTLKTLTTKSGTYG-YYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTRE 60
           +N+  TLK         G +Y L  LE+K    +SRLP SIR++LES+LRN DG +VT E
Sbjct: 3   RNTLNTLKEFKISGSRKGKFYSLPALEKKLGINISRLPVSIRIVLESVLRNCDGQKVTEE 62

Query: 61  DIEALARWRPDPGEIN-VPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVV 119
            ++ LA W       + +P  +ARV+LQDFTGVP + DLAAMR+     G +PK I P+V
Sbjct: 63  HVKQLASWSATGARTDEIPFVVARVVLQDFTGVPLLADLAAMRNVASKLGKNPKNIEPLV 122

Query: 120 PADLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVH 179
           P DLV+DHSVQ+D F    A   N++ E++RN ERY  +KW   A + F VVPPG GIVH
Sbjct: 123 PVDLVVDHSVQIDHFREKKALDLNMKLEFQRNNERYQFMKWGMQAFDTFGVVPPGFGIVH 182

Query: 180 QVNIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQP 239
           QVN+EYL +    G  +   + +PD+LVGTDSHTTM+NG+GV+GWGVGGIEAEA MLGQP
Sbjct: 183 QVNLEYLAR----GVHNKTGVYYPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQP 238

Query: 240 YYMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRA 299
            Y L P VVG  L G+L EG TATDLVLT+TE+LRK  VVGKFVEF+G G   LS  DRA
Sbjct: 239 VYFLTPDVVGVNLTGQLREGVTATDLVLTITELLRKTKVVGKFVEFFGEGTRSLSLTDRA 298

Query: 300 TIANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQY 359
           TIANMAPEYGATMGFFPVDE T++Y + TGR +  ++  E+Y KA  LF  P+A + + Y
Sbjct: 299 TIANMAPEYGATMGFFPVDEATISYFKGTGRTKAEIDAFESYFKAQNLFGIPKAGD-IDY 357

Query: 360 SEYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLV 419
           +  + LDL  V PSLAGPKRPQDR+ +  VK +F     KPV E GF    + L      
Sbjct: 358 TNEVSLDLGTVAPSLAGPKRPQDRIEIGNVKANFAELFVKPVAENGFNKKIEDLDATYT- 416

Query: 420 KRRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGS 479
               +  ++ +G V+IAAITSCTNTSNP+V+L AGLLAKKAVEAGL   P +KTSLAPGS
Sbjct: 417 --NTDGVKVKNGDVLIAAITSCTNTSNPNVLLAAGLLAKKAVEAGLKVSPHIKTSLAPGS 474

Query: 480 KVVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGN 539
           +VVT YLE +GL+P+LE LGF +  YGCTTCIGN+G L   + +A+ + ++V +AVLSGN
Sbjct: 475 RVVTKYLEAAGLLPYLEKLGFGVTAYGCTTCIGNAGDLTPAMNEAITKNDIVASAVLSGN 534

Query: 540 RNFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEE 599
           RNFE RI+P++++N+LASP LVVAYA+AG +++D  T+P+G    GK I+L DIWP+ +E
Sbjct: 535 RNFEARIHPNIRSNFLASPPLVVAYAIAGNVNVDLMTQPVGKGKGGKEIFLGDIWPTSQE 594

Query: 600 IREAIRKTLDPELFKKEYSKVFEGDER-WQALPA-PTGELYQWDPESTYIQNPPFFEDLG 657
           I + ++  ++ + FK+ Y+ V     + W+ +     GE+Y W P+STYI  PPFFE+  
Sbjct: 595 IEKLLKFAMNAKTFKENYADVKGAPGKLWEQIKGVAAGEVYDW-PKSTYIAEPPFFENFT 653

Query: 658 ERKVE---DIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSR 714
           E+       I GAR L V GDS+TTDHISPAG+I   SPAG++L++ GV   DFNSYGSR
Sbjct: 654 EQPTAAATGITGARALGVFGDSITTDHISPAGSIKDTSPAGKWLLANGVLKADFNSYGSR 713

Query: 715 RGNHEVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAG 774
           RGNHE+MMRGTFAN+RIKNLM+ G+EGG     P G+   +Y+ AM+Y  +G P +V  G
Sbjct: 714 RGNHEIMMRGTFANVRIKNLMVPGVEGGVTIHQPSGEEKSIYDAAMQYIGDGVPTMVFGG 773

Query: 775 KEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTG 834
           +EYGTGSSRDWAAKGT LLG++AV+  SFERIHRSNLVGMGVLPL+FL  ++ +TLG+TG
Sbjct: 774 EEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFLGNDSVQTLGITG 833

Query: 835 YEVYDILGLE-DLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLN 893
            E +D+ GLE ++KP++   +V  R++G     + + R+DTP+EVDYYK+GGIL  VL  
Sbjct: 834 EETFDLKGLEGEIKPQQEATLVIHRKNGETQEVKLLLRIDTPIEVDYYKHGGILPFVLRQ 893

Query: 894 ML 895
           +L
Sbjct: 894 LL 895


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: 2101
Number of extensions: 92
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