GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glucosaminate-lyase in Desulfovibrio vulgaris Hildenborough

Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 209312 DVU0377 thioredoxin reductase

Query= curated2:Q93HX6
         (320 letters)



>lcl|MicrobesOnline__882:209312 DVU0377 thioredoxin reductase
          Length = 305

 Score =  140 bits (354), Expect = 3e-38
 Identities = 106/311 (34%), Positives = 159/311 (51%), Gaps = 24/311 (7%)

Query: 9   VIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPALMER 68
           +IILG G AG ++A+YAARANL+ L++     GG +  T  V+N P     + G  L +R
Sbjct: 7   LIILGGGVAGMTSAIYAARANLRVLILDENACGGLVNWTKVVENMP-SYTSIGGMELAQR 65

Query: 69  MREHAERFETEI-VFDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARYLGLPSEEA 127
           M+E        +     I+++D       +  D   YT  A+I+ATG       +P E A
Sbjct: 66  MQEQVNNLGVTVEEAVCIDSMDLTGPEKRVEADGEVYTAKAVIVATGRKP----VPLEAA 121

Query: 128 FMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIA-STVTLIHRRETF----R 182
              + V  CA CDG  Y  K V VVGGGN+  +E+L L +   + +TL+ R + F    +
Sbjct: 122 GECEQVHFCAICDGAPYIGKRVLVVGGGNSGFDESLALLDQGIAELTLVERMDRFFAAQK 181

Query: 183 AEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNNDGSFDELKVDGVFIAI 242
           A+ +L  + NA +     +  ++ + DE L     VT   +    G     + DG+F+ +
Sbjct: 182 AQDLLAARPNATLMRSTEV--VSVDYDETL---RSVTLRDVAT--GEVFTREFDGIFVFM 234

Query: 243 GHTPNTSLFEGQLTL-KDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAG 301
           G  P T +F GQ  +   GY+V     D N  ATS+ G++AAGDV    YRQ  T+   G
Sbjct: 235 GQKPGTEVFRGQFDMDAQGYIVT----DEN-MATSLSGVYAAGDVRQKKYRQLTTAMADG 289

Query: 302 CMAALDTERYL 312
            MAAL+ ER++
Sbjct: 290 TMAALEAERFI 300


Lambda     K      H
   0.318    0.135    0.386 

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: 282
Number of extensions: 16
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: 320
Length of database: 305
Length adjustment: 27
Effective length of query: 293
Effective length of database: 278
Effective search space:    81454
Effective search space used:    81454
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: 48 (23.1 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 paper from 2022 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