Alignments for a candidate for acn in Rubrivirga marina SAORIC-28

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Rubrivirga marina SAORIC-28

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_095512259.1 BSZ37_RS20105 aconitate hydratase AcnA

Query= SwissProt::Q5SMF6
         (902 letters)



>NCBI__GCF_002283365.1:WP_095512259.1
          Length = 906

 Score = 1046 bits (2705), Expect = 0.0
 Identities = 536/893 (60%), Positives = 658/893 (73%), Gaps = 9/893 (1%)

Query: 5   FQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNED-GYQVTREDIE 63
           F    T+ T +G +  Y L  +     A++ RLPFSI+V+LE+ LR  D    V  +D+ 
Sbjct: 6   FDARDTIDTSAGAHTVYRLDRVAEATGADLDRLPFSIKVLLENALRQADLPGPVGEDDVR 65

Query: 64  ALARWRPD-PGEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPAD 122
            LA + P  P E+ +P   ARV+LQDFTGVPAVVDLAA+R A+   GGDP+ INP VP D
Sbjct: 66  NLATYDPAAPAEVEIPFTPARVLLQDFTGVPAVVDLAALRSAMARNGGDPEAINPRVPVD 125

Query: 123 LVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVN 182
           LVIDHSVQVD+F    AF  N + E++RN ERY  L+W   A +NF VVPP  GI HQVN
Sbjct: 126 LVIDHSVQVDSFALPQAFQINADIEFQRNAERYEFLRWGSKAFDNFSVVPPERGICHQVN 185

Query: 183 IEYLTKVVMTGKRD-GLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYY 241
           +EY+ + V T   D GL +A+PD+LVGTDSHTTM+NGLGVLGWGVGGIEAEA MLGQP Y
Sbjct: 186 LEYIARAVWTTPGDDGLPVAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPIY 245

Query: 242 MLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATI 301
           ML P+VVGF+L G+L EG TATDL LTVT+MLRKHGVVGKFVEF+G G++ +S PDRATI
Sbjct: 246 MLMPKVVGFRLNGKLKEGVTATDLTLTVTQMLRKHGVVGKFVEFFGTGLSSMSLPDRATI 305

Query: 302 ANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSE 361
           ANMAPEYGATMGFFP+D+ETL+YLR+T R E  VELVEAY KA GLFRT +  +  Q+  
Sbjct: 306 ANMAPEYGATMGFFPIDDETLDYLRRTNRDEATVELVEAYCKAQGLFRTDDTPDP-QFEA 364

Query: 362 YLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVKR 421
            LELDLS VEPS++GPKRPQDR+ L +V++ F A LT+P   +GFGL ED L      K 
Sbjct: 365 VLELDLSEVEPSMSGPKRPQDRIVLGDVQREFKASLTRPASPQGFGLKEDALDNTGAYKD 424

Query: 422 RD-EEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSK 480
            +  E +L HG VVIAAITSCTNTSNPSVML AGLLAKKAVE G+   P+VKTSLAPGS+
Sbjct: 425 DEGNELDLKHGDVVIAAITSCTNTSNPSVMLAAGLLAKKAVERGMTVPPYVKTSLAPGSR 484

Query: 481 VVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNR 540
           VVT YLE +GL  +L+ +G++LVGYGCTTCIGNSGPLPE +A+A+ +G+LVVA VLSGNR
Sbjct: 485 VVTAYLEKAGLQDYLDQIGYNLVGYGCTTCIGNSGPLPEPVAEAITDGDLVVAGVLSGNR 544

Query: 541 NFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEI 600
           NFEGRI+  VKANYLASP LVVAYALAG +DID   + +G D +G  +YLKD+WPS +EI
Sbjct: 545 NFEGRIHALVKANYLASPPLVVAYALAGTVDIDLQNDVIGQDQDGNDVYLKDLWPSQQEI 604

Query: 601 REAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGER- 659
            +AI + +  E F++ Y  + + + RW A+    G +Y W  +STYIQ PPFF D+    
Sbjct: 605 LDAINQAVTREQFEELYEGIEDSNPRWNAIDTSEGAVYDWQDDSTYIQEPPFFLDVTPEV 664

Query: 660 -KVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGNH 718
             +E IRGA+ L+  GDS TTDHISPAGAIP   PAGQYL   GV+P+DFNS+GSRRGN 
Sbjct: 665 PTIEPIRGAKTLVKAGDSTTTDHISPAGAIPKSEPAGQYLQDHGVEPKDFNSFGSRRGND 724

Query: 719 EVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGKEYG 778
            VM RGTF NIR++N +  G EGG+  K  +G+  ++Y+ A  Y AEGTPLLV AG +YG
Sbjct: 725 RVMTRGTFGNIRLRNQLAPGTEGGWTMK--DGEQMYIYDAAQEYAAEGTPLLVFAGVDYG 782

Query: 779 TGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGYEVY 838
            GSSRDWAAKGT LLGI AV+A+SFERIHRSNLVGMGVLPL F  GE+ +T GL G E +
Sbjct: 783 MGSSRDWAAKGTLLLGIEAVVAKSFERIHRSNLVGMGVLPLLFQDGESLDTHGLDGTEQF 842

Query: 839 DILGLEDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVL 891
           DI   +D++P + + + A + DGS V F     L+TPVEV+YY++GGIL  VL
Sbjct: 843 DIPVDDDVRPGQTLTVTATKGDGSTVAFDVTVALNTPVEVEYYRHGGILNYVL 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: 2282
Number of extensions: 107
Number of successful extensions: 7
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: 906
Length adjustment: 43
Effective length of query: 859
Effective length of database: 863
Effective search space:   741317
Effective search space used:   741317
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