Alignments for a candidate for acn in Thiomicrospira microaerophila ASL8-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Thiomicrospira microaerophila ASL8-2

Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_044409227.1 NA59_RS05490 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>NCBI__GCF_000934765.1:WP_044409227.1
          Length = 858

 Score = 1168 bits (3021), Expect = 0.0
 Identities = 586/858 (68%), Positives = 688/858 (80%), Gaps = 14/858 (1%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           MLE YR+ VAER  QGI   PLDA Q A ++ LLK P   E   L+DLL +RVPPGVDEA
Sbjct: 1   MLEAYRQLVAERELQGIPALPLDAQQTAEIINLLKQPNPAEVSVLVDLLTHRVPPGVDEA 60

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAK--LAPIAAKA 118
           AYVKA FLA VAK       ++PE+A  LLGTM GGYN+ PLI+ LD A   +A  A KA
Sbjct: 61  AYVKASFLADVAKESVKVEAIAPEQAAFLLGTMMGGYNVQPLIELLDSANKAVAETAMKA 120

Query: 119 LSHTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETN 178
           LS TLL++D ++DV EKA + N YAKQV++SWA+A+WF+ R PLA+KITVTVFKV GETN
Sbjct: 121 LSKTLLVYDAYHDVLEKADS-NSYAKQVVESWANADWFVDRKPLADKITVTVFKVDGETN 179

Query: 179 TDDLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGD 238
           TDDLSPA  AWSRPDIPLHA  ML +  E +    P ++  +K       KG+P+AYVGD
Sbjct: 180 TDDLSPATAAWSRPDIPLHAIEMLASKMENV----PQIIAELKA------KGHPVAYVGD 229

Query: 239 VVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298
           VVGTGSSRKSA NSV+W+ GDDIP VPNKR GG+ LGGKIAPIFFNT ED+G+LPIE DV
Sbjct: 230 VVGTGSSRKSAMNSVMWWFGDDIPYVPNKRQGGVVLGGKIAPIFFNTAEDSGSLPIECDV 289

Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
           S LNMGDVI +YPY+G++ N E G+ +++F+L    + DEVRAGGR+PLIIGR LT K R
Sbjct: 290 SQLNMGDVIHIYPYEGKITN-EAGDTISSFKLDPITMPDEVRAGGRVPLIIGRDLTDKTR 348

Query: 359 EALGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTG 418
            AL LP S+ F +  D   ++ G++LAQKMVG+ACGV G+RPG YCEP M +VGSQDTTG
Sbjct: 349 RALELPPSEHFIRPTDGDTATHGYTLAQKMVGQACGVAGVRPGVYCEPHMATVGSQDTTG 408

Query: 419 PMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGV 478
            MTRDE+K+LACLGFSAD V+QSFCHTAAYPKPVD+   H+LPDF+ +RGGVSLRPGDGV
Sbjct: 409 AMTRDEMKELACLGFSADFVLQSFCHTAAYPKPVDIKLQHSLPDFMTSRGGVSLRPGDGV 468

Query: 479 IHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKG 538
           IHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAF A  GVMPL+MPESVLVRFKG
Sbjct: 469 IHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFGATLGVMPLNMPESVLVRFKG 528

Query: 539 KMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDA 598
           KMQPGITLRDLV+AIP  AI+ GLLTVEKKGKKN+F+GR+LEIEGLPDLKVEQAFEL+DA
Sbjct: 529 KMQPGITLRDLVNAIPYQAIQSGLLTVEKKGKKNVFNGRVLEIEGLPDLKVEQAFELSDA 588

Query: 599 SAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQLL 658
           SAERSA GC +KL +  I+E+L SNI L++WM+  GY D RTL RR   M+KW+  P LL
Sbjct: 589 SAERSANGCVVKLGEASIIEFLKSNIRLIEWMVENGYQDARTLLRRRDEMQKWIDSPVLL 648

Query: 659 EADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFR 718
           EADADA+YA +I+IDL  IKEPI+  PNDPDD +LLS+V GEKIDEVFIGSCMTNIGH+R
Sbjct: 649 EADADAQYAEIIEIDLDQIKEPIVACPNDPDDVKLLSEVSGEKIDEVFIGSCMTNIGHYR 708

Query: 719 AAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQAR 778
           AAGK+L+N KG +PT+LW+APPT+MD  QL EEGYYS FG++GAR E+PGCSLCMGNQAR
Sbjct: 709 AAGKVLENIKGAVPTKLWIAPPTKMDERQLIEEGYYSTFGRTGARTEMPGCSLCMGNQAR 768

Query: 779 VADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAV 838
           VADGATV STSTRNFPNRLG  ANV+L SAELAAV A +GK+PT EEY   V+ +D  A 
Sbjct: 769 VADGATVFSTSTRNFPNRLGNDANVYLGSAELAAVIAAMGKIPTVEEYMAQVSMLDTMAD 828

Query: 839 DTYRYLNFDQLSQYTEKA 856
           D YRYL FD+++ Y  K+
Sbjct: 829 DVYRYLQFDEMADYEIKS 846


Lambda     K      H
   0.317    0.136    0.400 

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: 1980
Number of extensions: 70
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: 865
Length of database: 858
Length adjustment: 42
Effective length of query: 823
Effective length of database: 816
Effective search space:   671568
Effective search space used:   671568
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 (21.7 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