Alignments for a candidate for ilvD in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Cupriavidus basilensis 4G11

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate RR42_RS06125 RR42_RS06125 phosphogluconate dehydratase

Query= SwissProt::P55186
         (617 letters)



>FitnessBrowser__Cup4G11:RR42_RS06125
          Length = 628

 Score =  197 bits (502), Expect = 9e-55
 Identities = 184/594 (30%), Positives = 267/594 (44%), Gaps = 65/594 (10%)

Query: 37  IAVANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTI-AVDDGIAMGHGGMLYSLP 95
           + +  ++   +  H   +    ++     A G VA+    + A+ DGI  G+ GM  SL 
Sbjct: 72  LGIVTAYNDMLSAHQPYERYPGVIREAARAVGAVAQVAGGVPAMCDGITQGNAGMELSLF 131

Query: 96  SRDLIADSVEYMVNAHCADAIVCISNCDKITPGMLMAAMRL-NIPVVFVSGGPMEAGKVT 154
           SRD IA +    ++ +  DA V +  CDKI PG+LM A++  ++PVVFV  GPM  G ++
Sbjct: 132 SRDAIAMATAVSLSHNTFDAAVMLGVCDKIVPGLLMGALQFGHLPVVFVPAGPMSTG-LS 190

Query: 155 VKGKIRALDLVDAMVVAADDSYSDEEV--EAIEKAACPT---CGSCSGMFTANSMNCLTE 209
            K K R   L           Y+  +V  EA+ +A C      G+C+   TANS   L E
Sbjct: 191 NKEKARVRQL-----------YATGQVGREALLEAECEAYHGAGTCTFYGTANSNQFLME 239

Query: 210 ALGLSLPGNGSVLATHADREALFKEAGRVVVDLCQRWYEQEDATALPRGIATRAAFENAM 269
            +GL +PG   V      R+AL   A +  + L  R     D   L R +  RA     +
Sbjct: 240 IMGLHMPGAAFVHPDSGLRDALTAAAAQRALALTAR---GGDYLPLARIVDERAVINAVV 296

Query: 270 SLDIAMGGSTNTVLHLLAAAHEGGIDFSMADIDRLSRHVPCLSKVAPAKSDVHMEDVHRA 329
            L +A GGSTN  +HL+A A   GI     D DRLSR  P L++V P      +   H A
Sbjct: 297 GL-LATGGSTNHTIHLVAMARAAGILIDWDDFDRLSRITPLLARVYP-NGSADVNHFHAA 354

Query: 330 GGVMAILGELERGGLIDASQPTVHAPTMGEALARWDIGRTNSQIAHEFFKAAPGGKPTQV 389
           GGV  ++ +L   GL+     TV     G  LAR+                        V
Sbjct: 355 GGVAYVIRQLLSAGLLHEDVETV----AGRGLARY--------------------TQEPV 390

Query: 390 AFSQAARWEE-LDLDRENGVIRSVEHPFSKDGGLAVLFGNLAPEGCIVKTAGVDESILTF 448
                 +W +   +  +  V+ +   PFS +GGL +L GNL     ++K + V +     
Sbjct: 391 MIDGVLQWRDGAAVSGDATVLATAAEPFSAEGGLRLLQGNLGRG--MIKVSAVADEHRVV 448

Query: 449 RGTARVFESQDAAVSGILGGQVKAGEVVVIRYEGPKGGPGMQEMLYPTTYLKS-KGLGAA 507
              ARVF+SQ+   +    G+     + V+R++GP    GM E+   T  L S +  G  
Sbjct: 449 EAPARVFDSQEQLQAAFEAGEFTGDMIAVVRFQGPNAN-GMPELHRLTPVLGSLQDAGHK 507

Query: 508 CALVTDGRFSGGTSGL-SIGHVSPEAGEGGLIALVETGDPILIDIPTRGITLE-----VS 561
            ALVTDGR SG +  + ++ HV PEA  GG +A V  GD I +D      TLE       
Sbjct: 508 VALVTDGRMSGASGKVPAVIHVGPEALAGGPLARVRDGDRIRVDAVAG--TLEWLGAANG 565

Query: 562 DAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMTTNAARGAVRDVSQIE 615
           D  LA R  A L    DA+   +  R L    R  A +      G+  D+S+ +
Sbjct: 566 DGDLATRASAVLP--DDAFANFSVGRGLFGLFRRNARIAEEG--GSALDLSEAD 615


Lambda     K      H
   0.318    0.134    0.395 

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: 1075
Number of extensions: 60
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 617
Length of database: 628
Length adjustment: 37
Effective length of query: 580
Effective length of database: 591
Effective search space:   342780
Effective search space used:   342780
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: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis