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

GapMind for catabolism of small carbon sources

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

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_095512259.1 BSZ37_RS20105 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_002283365.1:WP_095512259.1
          Length = 906

 Score =  675 bits (1742), Expect = 0.0
 Identities = 373/875 (42%), Positives = 521/875 (59%), Gaps = 51/875 (5%)

Query: 37  KLPYTSRVLAENLVRRCE------PEMLTASLKQIIESKQELDFPWFPARVVCHDILGQT 90
           +LP++ +VL EN +R+ +       + +         +  E++ P+ PARV+  D  G  
Sbjct: 37  RLPFSIKVLLENALRQADLPGPVGEDDVRNLATYDPAAPAEVEIPFTPARVLLQDFTGVP 96

Query: 91  ALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNE 150
           A+VDLA LR A+A  GGDP  +NP VP  L++DHS+ V+     + AF  N  IE +RN 
Sbjct: 97  AVVDLAALRSAMARNGGDPEAINPRVPVDLVIDHSVQVDSFALPQ-AFQINADIEFQRNA 155

Query: 151 DRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNG-----VAFPDTLVGTDS 205
           +R+ F+ W  KAF N  V+P   GI HQ+NLE ++  +    G     VA+PDTLVGTDS
Sbjct: 156 ERYEFLRWGSKAFDNFSVVPPERGICHQVNLEYIARAVWTTPGDDGLPVAYPDTLVGTDS 215

Query: 206 HTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTE 265
           HT  ++ LGV+  GVGG+EAE+ MLG+  YM +P ++G  L GK + G+TATD+ L +T+
Sbjct: 216 HTTMINGLGVLGWGVGGIEAEAAMLGQPIYMLMPKVVGFRLNGKLKEGVTATDLTLTVTQ 275

Query: 266 FLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGRE 325
            LR   VV  ++EFFG G  +++L DRATI+NM PE+GAT   F ID +TLDYL  T R+
Sbjct: 276 MLRKHGVVGKFVEFFGTGLSSMSLPDRATIANMAPEYGATMGFFPIDDETLDYLRRTNRD 335

Query: 326 AEQVKLVETYAKTAGLW-SDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSELAAR 384
              V+LVE Y K  GL+ +DD     +   L  DLS V  +++GP  P  R+   ++   
Sbjct: 336 EATVELVEAYCKAQGLFRTDDTPDPQFEAVLELDLSEVEPSMSGPKRPQDRIVLGDVQRE 395

Query: 385 --------------GISGEVENEPGLMPD----------GAVIIAAITSCTNTSNPRNVI 420
                         G+  +  +  G   D          G V+IAAITSCTNTSNP  ++
Sbjct: 396 FKASLTRPASPQGFGLKEDALDNTGAYKDDEGNELDLKHGDVVIAAITSCTNTSNPSVML 455

Query: 421 AAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCN 480
           AAGLLA+ A  +G+T  P+VKTSLAPGS+ V  YLE+A L   L+ +G+ +VG+ CTTC 
Sbjct: 456 AAGLLAKKAVERGMTVPPYVKTSLAPGSRVVTAYLEKAGLQDYLDQIGYNLVGYGCTTCI 515

Query: 481 GMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIR 540
           G SG L   + + + D DL    VLSGNRNF+GRIH   K  +LASPPLVVAYA+AGT+ 
Sbjct: 516 GNSGPLPEPVAEAITDGDLVVAGVLSGNRNFEGRIHALVKANYLASPPLVVAYALAGTVD 575

Query: 541 FDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYG--- 597
            D++ DV+G D+DG  V L ++WPS  EI   I  +V  EQF ++YE + D +  +    
Sbjct: 576 IDLQNDVIGQDQDGNDVYLKDLWPSQQEILDAINQAVTREQFEELYEGIEDSNPRWNAID 635

Query: 598 DKVSPLYDWRPQSTYIRRPPYWEGALAGERT---LKGMRPLAVLGDNITTDHLSPSNAIM 654
                +YDW+  STYI+ PP++        T   ++G + L   GD+ TTDH+SP+ AI 
Sbjct: 636 TSEGAVYDWQDDSTYIQEPPFFLDVTPEVPTIEPIRGAKTLVKAGDSTTTDHISPAGAIP 695

Query: 655 MDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLAR 714
               AG+YL   G+  +DFNS+ + RG+     R TF N +L+N++A       +G    
Sbjct: 696 KSEPAGQYLQDHGVEPKDFNSFGSRRGNDRVMTRGTFGNIRLRNQLA----PGTEGGWTM 751

Query: 715 IEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFER 774
            + E +   +++A + Y     PL++ AG DYG GSSRDWAAKG  L G+EA+VA+ FER
Sbjct: 752 KDGEQMY--IYDAAQEYAAEGTPLLVFAGVDYGMGSSRDWAAKGTLLLGIEAVVAKSFER 809

Query: 775 IHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFD--VIGSIAPRADLTVIITRKNGERVE 832
           IHR+NLVGMGVLPL F+ GE+  T+G+DGTE FD  V   + P   LTV  T+ +G  V 
Sbjct: 810 IHRSNLVGMGVLPLLFQDGESLDTHGLDGTEQFDIPVDDDVRPGQTLTVTATKGDGSTVA 869

Query: 833 VPVTCRLDTAEEVSIYEAGGVLQRFAQDFLESNLK 867
             VT  L+T  EV  Y  GG+L    +D++   L+
Sbjct: 870 FDVTVALNTPVEVEYYRHGGILNYVLRDYMAGELE 904


Lambda     K      H
   0.318    0.136    0.397 

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: 2052
Number of extensions: 114
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: 867
Length of database: 906
Length adjustment: 43
Effective length of query: 824
Effective length of database: 863
Effective search space:   711112
Effective search space used:   711112
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