Alignments for a candidate for acn in Amphritea japonica JAMM 1866

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Amphritea japonica JAMM 1866

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_019622309.1 G329_RS0112385 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>NCBI__GCF_000381785.1:WP_019622309.1
          Length = 931

 Score =  327 bits (839), Expect = 2e-93
 Identities = 283/911 (31%), Positives = 432/911 (47%), Gaps = 109/911 (11%)

Query: 16  GIVPKPLDATQMAALVELLKTPPVGEE--EFLLDLLINRVPPGVDEAAYVKAGFLAAVAK 73
           G+ PKP+D+ ++ + + + +   VG E  E  L+  I  + PG   AA VKA FL  +A 
Sbjct: 19  GLNPKPIDSAELLSEI-IAQIKDVGNEHREASLNFFIYNILPGTTPAAGVKATFLKDIAL 77

Query: 74  GDTTSPLVSPEKAIELLGTMQGGYNIHPLID-ALDDAKLAPIAAKALSHTLLMFD-NFYD 131
           G  T   +S E A+E L  M+GG ++  L+D AL D   A  AA+ L   + ++D +   
Sbjct: 78  GKETVAEISAEFALEQLSHMKGGPSVEALLDIALSDDAQAAAAAEVLKSQVFLYDADSAR 137

Query: 132 VEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITV-TVFKVTGETNTDDLSPAPDAWS 190
           + +  KAGN  AK +++S++ AE+F     + E I V T     G+ +TD LSP   + S
Sbjct: 138 LADAFKAGNAIAKDILESYSKAEFFTKLSDIPETIKVITYIAGEGDISTDLLSPGNQSHS 197

Query: 191 RPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVVGTGSSRKSAT 250
           R D  LH + M+    +  E  + G   P  ++  + +KG         +G GSSR S  
Sbjct: 198 RADRELHGKCMISPEAQQ-EIAEMGKQNPDAKVMLIAEKG--------TMGVGSSRMSGV 248

Query: 251 NSV-LWFMGDDIPNVPNKRGGGLCLGGK-IAPIFFNTM---------------------- 286
           N+V LW      P +P      +  G   IAPIF  T+                      
Sbjct: 249 NNVALWAGEKTSPYIPFINNNPVVAGTNGIAPIFLTTVGVTGGIGLDLKNWVKKTDANGE 308

Query: 287 --EDAGALPIEVDVSNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGR 344
              DA   P+  +  ++  G V+ +     ++ N +  EL+   +  T   ++ ++AGG 
Sbjct: 309 VVRDANGDPVLEEAYSVATGTVLTIDTKAKKLYNGDQ-ELVDIADAFTPQKVEFMKAGGS 367

Query: 345 IPLIIGRGLTTKAREALGLPHSDVFRQAKDVAESSRGFSLAQKMVGR-ACGVKGIRP--- 400
             +  G+ L T A E LG+    V+ Q+K+++   +G +  +K+  R A GV    P   
Sbjct: 368 YAVTFGKKLQTFAAETLGVEAPAVYAQSKEISHEGQGLTAVEKIFNRNAVGVTSKTPLHT 427

Query: 401 GAYCEPKMTSVGSQDTTGPMTRDELKDLAC--LGFSADLVMQSFCHTAAYPKPVDVTTHH 458
           G+    K+  VGSQDTTGPMT  EL+ +A   +  S D   QS CHTA+           
Sbjct: 428 GSDVRVKVNIVGSQDTTGPMTCQELEAMAASTISTSVDGAFQSGCHTASVWDNKAKANTP 487

Query: 459 TLPDFIMNRGGVSLRPGDGVIHSW-------LNRMLLPD-TVGTGGDSHTRFPIGISFPA 510
            L  F+   G ++ R    V HS        LN + + D  +  GGDSHTR   G++F A
Sbjct: 488 KLMAFMNAFGAITARDPKHVYHSMTDVIHKVLNDITVDDRAIIIGGDSHTRMSKGVAFGA 547

Query: 511 GSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGK 570
            SG VA A ATG   + +PESV V FKG M+P +  RD+VHA     +K       K G 
Sbjct: 548 DSGTVAIALATGESAMPIPESVKVTFKGSMKPHMDFRDIVHATQAQMLK-------KFGG 600

Query: 571 KNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWM 630
           +N+F GR++E++ +  L  +QAF  TD +AE  A         + +++ L      ++ M
Sbjct: 601 ENVFQGRVIEVQ-IGTLLADQAFTFTDWTAEMKAKASICISTDDTLIQSLELAKSRIQIM 659

Query: 631 IAEGY-GDRRTLERRIQGMEKWLADPQLLEA-----DADAEYAAVIDIDLADIKEPILCA 684
           I +G   +   L+  I   +K +A+ +  EA     D +A+Y A + +DL  I+EP++  
Sbjct: 660 INKGMENEAGMLQGLIDLADKRIAEVKSGEAPALAPDDNAKYYAELVVDLDVIEEPMIAD 719

Query: 685 P---NDPDDARLLSDV-------QGEKIDEVFIGSCMTNIGHFRAAGKLLDN--HKGQLP 732
           P   N+    R   DV        G K+D  F+GSCM + G  +    +L N   KG + 
Sbjct: 720 PDVNNEDVSKRYTHDVIRPASYYDGRKVDLGFVGSCMVHKGDMQIIAAMLRNLEKKGPIT 779

Query: 733 TR--LWVAPPTRMDAAQLTEEGYYSVF------------GKSGAR--------IEIPGCS 770
            +  L VAPPT     +L  EG + +              K  AR        +E PGC+
Sbjct: 780 FKAPLVVAPPTYNIVDELKAEGDWELLEKFAGFEFSDENPKEAARTKYENILYLERPGCN 839

Query: 771 LCMGNQARVADGATVVSTSTRNFPNRL-----GTGANVFLASAELAAVAALIGKLPTPEE 825
           LCMGNQ +   G TV++TSTR F  R+            L S  +  ++ ++G+ PT EE
Sbjct: 840 LCMGNQEKAEAGDTVLATSTRLFQGRVVEDTAEKKGESLLGSTPMVVLSCVLGRFPTLEE 899

Query: 826 YQTYVAQVDKT 836
           Y+  V  +D T
Sbjct: 900 YKEAVEGIDLT 910


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: 1710
Number of extensions: 85
Number of successful extensions: 12
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: 931
Length adjustment: 43
Effective length of query: 822
Effective length of database: 888
Effective search space:   729936
Effective search space used:   729936
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