GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Epibacterium ulvae U95

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_090218033.1 CV091_RS10640 aldehyde dehydrogenase family protein

Query= curated2:Q2SXN9
         (487 letters)



>NCBI__GCF_002796795.1:WP_090218033.1
          Length = 483

 Score =  186 bits (473), Expect = 1e-51
 Identities = 141/455 (30%), Positives = 220/455 (48%), Gaps = 20/455 (4%)

Query: 6   IDGAWVDGAGPVFASRNPGT-NERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64
           I G+W  G   +  +RNP   ++ V   A AS+D ++  +  A+ A A W+A  ++ +  
Sbjct: 9   IAGSWTVGVDEI-ENRNPSDLSDLVGMFAQASSDQLDATLDQAKIAQAEWAAYGIERKYN 67

Query: 65  IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124
           ++      ++ R E L T++ RE GKPL E + EV                + GE    +
Sbjct: 68  VLMAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFFTYYAAETLRQIGENADSV 127

Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183
            +G+ + +R    G VA+  P+NFP    +  I PAL  GN VV+KP+   P  A A  E
Sbjct: 128 REGIEIDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANATPASAVALTE 187

Query: 184 IWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242
           I     +P G+ +LV G  ++ G  L    ++D + FTGS   G  +      +    + 
Sbjct: 188 IIERQDIPKGLFSLVMGAGREIGQRLVESSKVDAISFTGSVPVGKGIASA-AIQNLTKVQ 246

Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302
           +EMG  N L V +  DID AV  A+  AF   GQ+CT + R++V   A  D FV++L   
Sbjct: 247 MEMGSKNALAVMDDADIDLAVSLALGGAFGGTGQKCTASSRLVV-HSAVHDEFVSKLVAG 305

Query: 303 ASKITAS-VFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEM-----KQRDPAL 356
           A  +      +A  Q  +G V++ +  +  +A     V LG S   E+     +   P  
Sbjct: 306 AKAMKVGHALEAGTQ--IGPVVTEQQLNENLA----YVDLGKSEGAELLCGGQRLEMPHQ 359

Query: 357 GF-VNAAI-LDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQ 414
           G+ +N  I +  TN   +  EE F PLA +++ +  D+A++  NDT FGL++G++     
Sbjct: 360 GYYMNPGIFIGTTNDMRINREEMFAPLAAVIKVSGYDEALSVVNDTNFGLTSGIVTKSLA 419

Query: 415 AWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRS 449
             + FRR  + G V  N PT G     PFGG G S
Sbjct: 420 RANHFRRNAQTGCVMVNLPTAGTDYHVPFGGRGDS 454


Lambda     K      H
   0.320    0.134    0.402 

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: 441
Number of extensions: 21
Number of successful extensions: 3
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: 487
Length of database: 483
Length adjustment: 34
Effective length of query: 453
Effective length of database: 449
Effective search space:   203397
Effective search space used:   203397
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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