Alignments for a candidate for acn in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Desulfovibrio vulgaris Miyazaki F

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 8502313 DvMF_3021 aconitate hydratase (RefSeq)

Query= SwissProt::Q5SMF6
         (902 letters)



>FitnessBrowser__Miya:8502313
          Length = 641

 Score =  219 bits (559), Expect = 3e-61
 Identities = 200/664 (30%), Positives = 269/664 (40%), Gaps = 171/664 (25%)

Query: 172 PPGTGIVHQVNIEYLTKVVMTGKRDGLTLAFPDS-LVGTDSHTTMVNGLGVLGWGVGGIE 230
           PPGTGI HQ+++E                A P + LVG+DSHT    G+G L  G GG+ 
Sbjct: 94  PPGTGICHQLHLE--------------NFALPGATLVGSDSHTPTAGGIGSLAMGAGGLS 139

Query: 231 AEAVMLGQPYYMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGV 290
               M G+PY++  PRVV  +L G L   A+A D++L +  +L   G VGK  EF GPGV
Sbjct: 140 VALAMAGEPYFISMPRVVRVRLEGRLTGWASAKDVILHLLGLLTVKGGVGKVFEFAGPGV 199

Query: 291 AKLSTPDRATIANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRT 350
           A LS P+RA I NM  E GAT   FP DE T  +L    R               G ++ 
Sbjct: 200 ATLSVPERAVITNMGAELGATASLFPSDERTRAFLASMDRE--------------GDWKP 245

Query: 351 PEAEEKVQYSEYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSE 410
             A+    Y + + +DLSA+ P +A P  P   VP+ E+                 GLS 
Sbjct: 246 LAADADATYDDEIVIDLSALVPLVAQPHMPDRVVPVAELA----------------GLSV 289

Query: 411 DQLQRKVLVKRRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPW 470
           DQ+                       AI SCTN+S   + + A +L  + V  G D    
Sbjct: 290 DQV-----------------------AIGSCTNSSYADMRMVAEVLRGRMVHVGTD---- 322

Query: 471 VKTSLAPGSKVVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNL 530
             T ++PGSK V   L   GL+  L   G  ++   C  CIG  G         V  G  
Sbjct: 323 --TMVSPGSKQVLKMLAAEGLVEPLLDAGVRILECSCGPCIGMGG-------SPVSGG-- 371

Query: 531 VVAAVLSGNRNFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYL 590
              +V + NRNFEGR        YL SP+     AL G+      T+P  +   G P   
Sbjct: 372 --VSVRTFNRNFEGRSGTKDAKVYLVSPLTAAMAALHGQF-----TDPATW---GTPPAQ 421

Query: 591 KDIWPSMEEIREAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNP 650
            ++      IR                           A P   G   +       ++ P
Sbjct: 422 PELPAKAPSIRHLF------------------------AFPPRDGSGVE------VLRGP 451

Query: 651 PFFEDLGERKVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNS 710
                     ++D   A V++ LGD +TTDHI PAGA                       
Sbjct: 452 NIVALEQFTPMDDTVAAPVVIKLGDDITTDHIMPAGA----------------------E 489

Query: 711 YGSRRGNHEVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLL 770
             S R N   + +  F  +                     D DFV     R +A G   +
Sbjct: 490 ITSLRSNVPAIAQHVFGRV---------------------DADFV----ARARAAGIG-V 523

Query: 771 VIAGKEYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETL 830
           ++AG  YG GSSR+ AA     LGIRAV+  S  RIHR+NLV  G+LPL      + + L
Sbjct: 524 IVAGDNYGQGSSREHAALAPRHLGIRAVIVRSLARIHRANLVNFGILPLILCDRTDYDKL 583

Query: 831 GLTG 834
            + G
Sbjct: 584 AVGG 587


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: 1274
Number of extensions: 75
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 902
Length of database: 641
Length adjustment: 40
Effective length of query: 862
Effective length of database: 601
Effective search space:   518062
Effective search space used:   518062
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: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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