GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Desulfovibrio vulgaris Miyazaki F

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 8501918 DvMF_2633 Aldehyde Dehydrogenase (RefSeq)

Query= metacyc::MONOMER-13349
         (490 letters)



>FitnessBrowser__Miya:8501918
          Length = 460

 Score =  122 bits (305), Expect = 3e-32
 Identities = 104/351 (29%), Positives = 164/351 (46%), Gaps = 24/351 (6%)

Query: 133 RALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEETPGTATLLAEVM 192
           +A +Y  R+PLG V   + W  P   L   +A A+  GNAVV +PS E P TA ++  ++
Sbjct: 92  KARSYVRRQPLGRVVAYAHWADPFRSLLVPLADAIGAGNAVVLRPSAEAPATAEMVTRMV 151

Query: 193 HTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRAAATHVKPVSFE 252
                P  V   V G G ++    + T  D   + + G++R    I   AA  + P +  
Sbjct: 152 RQYFEPEHV--AVVGGGAETDEALLATAPDF--VWYDGDARGARTIAVLAAPTLTPYAAI 207

Query: 253 LGGKNAAIIFADCDFEKMIDGMMRAVFLHSGQVCLCAERVYVERPIYNRFLDAFVERVKA 312
            GG +AA++  D D       ++ A FLH+GQ+    + + V+R + +R LDA   R + 
Sbjct: 208 TGGPSAALVHGDADMAMAARRIVWAKFLHAGQLRAAPDVLLVQRTVLDRVLDAL--RTEL 265

Query: 313 LKLGWPQDGTTG-MGPLISAEHRDKVLSYFKLAREEGAQVLVGGGVP-KFGDARD----A 366
            +   PQ  T+   G ++SA            AR +  ++ +G  +P   GDA +    A
Sbjct: 266 ERAFGPQPRTSADFGRMVSAA---------GFAR-QAERLAIGRALPFGPGDAANQPDRA 315

Query: 367 GFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKYGLSATTWTGNLN 426
             +V PT++T +P  +  ++EE FGP+  V P+    EA A         +   +T    
Sbjct: 316 SLYVPPTLLTDVPDDSPVLREEGFGPVLVVRPYTRLDEATAFLAGLPALTALYAFTTAHA 375

Query: 427 RGHRVSEAMRVGLSWVN--SWFLRDLRTPFGGVGLSGIGREGGMHSLNFYS 475
           RG R+ E  R G   +N  +  L + R P GGVG +G G   G   L  +S
Sbjct: 376 RGERLMENTRAGAVLINDAATHLANPRLPQGGVGETGHGAMAGPAGLATFS 426


Lambda     K      H
   0.321    0.137    0.420 

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: 542
Number of extensions: 29
Number of successful extensions: 4
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: 490
Length of database: 460
Length adjustment: 33
Effective length of query: 457
Effective length of database: 427
Effective search space:   195139
Effective search space used:   195139
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 (21.8 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