GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Sinorhizobium meliloti 1021

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; EC 1.1.1.401 (characterized)
to candidate SMc01214 SMc01214 zinc-containing alcohol dehydrogenase

Query= SwissProt::P0DOW0
         (331 letters)



>FitnessBrowser__Smeli:SMc01214
          Length = 347

 Score =  153 bits (386), Expect = 7e-42
 Identities = 105/327 (32%), Positives = 165/327 (50%), Gaps = 21/327 (6%)

Query: 1   MKTLTWTAKETMSILSAPAPVPEPGWIALRVAGVGICGSELSGYLGHNELRK-PPLVMGH 59
           MK +   +   +S+ +   P P P  + ++V   GICG++   +L H E    PP+ +GH
Sbjct: 1   MKAVRLESVGNISVRNVGIPEPGPDDLLVKVEACGICGTDR--HLLHGEFPSTPPVTLGH 58

Query: 60  EFSGVVEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIGIDFPGAYAE 119
           EF G+V E G  V ++  G  +T +P ++CGRC  C  G    C + R IGI   G +AE
Sbjct: 59  EFCGIVVEAGSAVRDIAPGARITGDPNISCGRCPQCQAGRVNLCRNLRAIGIHRDGGFAE 118

Query: 120 RVLVPSNQCYAVK---DAIDGALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTVRL 176
            VLVP  Q + +    D + GA  EPLAC +  V L+ IK G T  ++G G+IGL+TV+L
Sbjct: 119 YVLVPRKQAFEIPLTLDPVHGAFCEPLACCLHGVDLSGIKAGSTVAILGGGVIGLLTVQL 178

Query: 177 LGLSGAKRIAVVDPNDERLKISQLWGAT-EMAPNLGALL------TDNHPQSFDCVIDAV 229
             L+GA  + +      + ++++  GAT  + P+ G ++          P   D VI+  
Sbjct: 179 ARLAGATTVILSTRQATKRRLAEEVGATATVDPSAGDVVEAIAGPVGLVPGGVDVVIECA 238

Query: 230 GLSTTRRDSLNALIRGGRAVWIGL--HEALTHLDGNQIVRDELEVRGSFCYTDDEFI--R 285
           G++ T + S      GG  V +G+        ++   I+  EL V GSF    + F+  R
Sbjct: 239 GVAETVKQSTRLAKAGGTVVILGVLPQGEKVEIEPFDILFRELRVLGSFI---NPFVHRR 295

Query: 286 AVSLINSQKFLPVDRQWLDVRSLEEGP 312
           A  L+ +   + +DR      SL+E P
Sbjct: 296 AADLV-ATGAIEIDRMISRRISLDEAP 321


Lambda     K      H
   0.322    0.139    0.424 

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: 365
Number of extensions: 22
Number of successful extensions: 3
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: 331
Length of database: 347
Length adjustment: 28
Effective length of query: 303
Effective length of database: 319
Effective search space:    96657
Effective search space used:    96657
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 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