GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Sinorhizobium meliloti 1021

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate SMa1296 SMa1296 alcohol dehydrogenase

Query= BRENDA::Q8L3C9
         (344 letters)



>FitnessBrowser__Smeli:SMa1296
          Length = 340

 Score =  451 bits (1160), Expect = e-131
 Identities = 217/337 (64%), Positives = 268/337 (79%)

Query: 5   TMKAAVIREFGSLLKIEEVEVKRPGRNEILVKVIASGVCHTDLHAVEGDWPVKPKMPLIP 64
           TM AAV+REFG  L IEEV V +PG  ++L+K  A+GVCHTDLHA +GDWPV+P  P IP
Sbjct: 2   TMTAAVVREFGKPLVIEEVPVPQPGPGQVLIKYEATGVCHTDLHAAKGDWPVRPNPPFIP 61

Query: 65  GHEAVGYVVAVGQEVKNVKEGDAVGVPWLYSACGGCDQCITGWETLCDTQQNGGYSVDGG 124
           GHE VGYV  +G EV  +KEGD VGVPWL++ACG C  C TGWETLC +QQN GYSVDG 
Sbjct: 62  GHEGVGYVAKLGAEVTRLKEGDRVGVPWLHTACGCCTPCRTGWETLCGSQQNTGYSVDGT 121

Query: 125 FAEYVIADARYVGLLPSNVNFMEMAPILCAGVTVYKGLKETEVKPGEWVAISGIGGLGHV 184
           FA+Y +AD  +VG LP+ + F   AP+LCAGVTVYKGLKETEV+PGEWV +SGIGGLGH+
Sbjct: 122 FAQYGLADPDFVGRLPARLEFGPAAPVLCAGVTVYKGLKETEVRPGEWVLVSGIGGLGHM 181

Query: 185 AVQYAKAMGMHVAAIDVADDKLDLAKKLGADLVVNAKNQNPGEFLKKEVGGMHGALITAV 244
           AVQYAKAMGMHVAA D+  DKL LA+KLGADLVV+A+  +  E +++  GG+HGAL+TAV
Sbjct: 182 AVQYAKAMGMHVAAADIFPDKLALAEKLGADLVVDARAPDAVEEVQRRTGGLHGALVTAV 241

Query: 245 SPIAFKQGLETLRRKGTMALNGLPPGNFDLSIFDTVLNRITIRGSIVGTRKDMKEAIEFA 304
           SP A +Q    LR KGTMAL GLPPG   L +FDTVL RIT+RGSIVGTR+D++EA+EFA
Sbjct: 242 SPKAMEQAYSMLRSKGTMALVGLPPGQICLPVFDTVLKRITVRGSIVGTRQDLEEALEFA 301

Query: 305 VEGKVKATVTPAKLENINEVFDKMKKGQIEGRVVLEI 341
            EGKV A  +  K+ENIN +F++M++G+I+GR+VL++
Sbjct: 302 GEGKVAAHFSWDKIENINAIFERMEEGKIDGRIVLDL 338


Lambda     K      H
   0.318    0.137    0.404 

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: 415
Number of extensions: 8
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: 344
Length of database: 340
Length adjustment: 29
Effective length of query: 315
Effective length of database: 311
Effective search space:    97965
Effective search space used:    97965
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: 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