Aligments for a candidate for nbaE in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Aligments for a candidate for nbaE 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources