GapMind for catabolism of small carbon sources

 

Aligments for a candidate for sdh in Sinorhizobium meliloti 1021

Align L-iditol 2-dehydrogenase (EC 1.1.1.14); D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate SMc01992 SMc01992 alcohol dehydrogenase

Query= reanno::HerbieS:HSERO_RS17015
         (345 letters)



>lcl|FitnessBrowser__Smeli:SMc01992 SMc01992 alcohol dehydrogenase
          Length = 346

 Score =  414 bits (1065), Expect = e-120
 Identities = 203/342 (59%), Positives = 253/342 (73%)

Query: 2   QALVLEATRELKLREIDLPQQMGAQDVRIRIHTVGICGSDLHYYTHGSIGPFKVEAPMVL 61
           +ALVLE   +L LR+I + + +   DV I I TVG+CGSD+HYYTHG IGPF V  PM+L
Sbjct: 3   KALVLEKKGQLSLRDIPVRRDLSPTDVLIGIRTVGVCGSDVHYYTHGKIGPFVVNEPMIL 62

Query: 62  GHEASGTVIEVGSAVSHLKVGDRVCMEPGIPRLDSPATLRGMYNLDPAVRFWATPPIHGC 121
           GHEA+G V+EVGS V HLK GDRVCMEPGIP L S ++  G+YN+DP+VRFWATPP+HGC
Sbjct: 63  GHEAAGVVLEVGSQVRHLKKGDRVCMEPGIPDLSSRSSKLGIYNVDPSVRFWATPPVHGC 122

Query: 122 LTGSVVHPAAFTYRLPDNVSFAEGAIVEPLSIGLQAATKARMKPGDTAVVIGAGTIGAMT 181
           LT  VVHPAAFTYRLPD+VSFAEGA+VEP +IG+QAA +A ++PGD   V+GAG IG MT
Sbjct: 123 LTPEVVHPAAFTYRLPDHVSFAEGAMVEPFAIGVQAALRAGIRPGDVGAVMGAGPIGMMT 182

Query: 182 ALAALAGGAARVILADVVAEKLAHFADNPAVITVDVTRETLTDVVRQATDGWGADVVFEA 241
           ALAALAGG ++V +AD+   KL        + T++V ++ +++ +  AT GWGADVVFE 
Sbjct: 183 ALAALAGGCSKVYVADLAQPKLDVIGAYEGIETINVRQQAVSEALAGATGGWGADVVFEC 242

Query: 242 SGHAGVYQTLLDLVCPGGCAVLVGMPPAPVALDVVAMQTKEVRLESVFRYANIFPRALAL 301
           SG A     L  L  PGG  VLVGMP  PV  D+V MQ KE+R+E+VFRYAN++ RA+ L
Sbjct: 243 SGAAPAILALPSLARPGGTVVLVGMPVEPVPFDIVGMQAKELRIETVFRYANVYDRAIEL 302

Query: 302 ISSGMIDVKPFISRKFPFSQSIRAFEEAASGRPQDVKIQIEM 343
           I+SG +D+KP IS   PF +SI AF+ A   RP DVKIQIEM
Sbjct: 303 IASGKVDLKPLISATIPFDESIAAFDRAVEARPTDVKIQIEM 344


Lambda     K      H
   0.321    0.137    0.403 

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: 383
Number of extensions: 14
Number of successful extensions: 1
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: 345
Length of database: 346
Length adjustment: 29
Effective length of query: 316
Effective length of database: 317
Effective search space:   100172
Effective search space used:   100172
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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