GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucD in Cupriavidus basilensis 4G11

Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate RR42_RS26650 RR42_RS26650 galactarate dehydratase

Query= reanno::BFirm:BPHYT_RS34230
         (431 letters)



>FitnessBrowser__Cup4G11:RR42_RS26650
          Length = 507

 Score =  209 bits (533), Expect = 1e-58
 Identities = 139/408 (34%), Positives = 203/408 (49%), Gaps = 36/408 (8%)

Query: 5   AQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFR-EPLDAFDDPSAEREPP 63
           A++ T  G++R DGR G RN + +   V C+  V R I   F  E + A+ +        
Sbjct: 105 AERATFMGFVRPDGRVGTRNFIGILSSVNCSATVIRHIADHFTPERMAAYPNVDGVAA-- 162

Query: 64  VHLIGFPGCYPNGYAE------KMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVR-AS 116
                  GC  +  +E      + L     HPN+  VL V LGCE      L++      
Sbjct: 163 --FAQSSGCGMSSPSEHFDVLRRTLAGYARHPNLAGVLIVGLGCERNQVAGLMESQGLVP 220

Query: 117 GRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSG 176
           G  V  + +Q+ GGT +TIQ G+  I           + P+  S L IG  CGGSDG SG
Sbjct: 221 GSHVRTMVMQDSGGTAATIQAGIRAIEAMLPGANTATRQPVPASHLKIGLECGGSDGFSG 280

Query: 177 ITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVA------ 230
           I+ANPA+G A D L+  G T I  ET E+ G E+ +  RA  P +G +++  +A      
Sbjct: 281 ISANPALGAAMDILVRHGGTAILSETPEIHGVEYMLTRRAVTPEVGQKLLDRLAWWERYT 340

Query: 231 --KAARYYSILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLY 288
             + A++  ++GH     GN  GGL    EKSLG+  K G +P+  + +  +     G  
Sbjct: 341 AGQNAQFNGVVGH-----GNQQGGLANIFEKSLGSAMKGGTTPLQAVYEYAEPIEQSGFV 395

Query: 289 LLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPAT 348
            +D           P     A  G+ IA GA++I FTTGRGS+ GS  +P IK+ +N   
Sbjct: 396 FMD----------SPGYDPVAATGQ-IASGANLICFTTGRGSMFGSKPAPTIKLASNTPM 444

Query: 349 YRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLG 396
           Y  L GDMD++ G +L+G  T+DE+G+ +FE  +  + G  +KSE LG
Sbjct: 445 YTRLEGDMDINCGLVLDGELTVDEMGQRIFEHILEAASGHPTKSEALG 492


Lambda     K      H
   0.318    0.137    0.408 

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: 589
Number of extensions: 36
Number of successful extensions: 5
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: 431
Length of database: 507
Length adjustment: 33
Effective length of query: 398
Effective length of database: 474
Effective search space:   188652
Effective search space used:   188652
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: 51 (24.3 bits)

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

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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:

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:

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:

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:

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