GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Lactobacillus silagei IWT126

Align succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized)
to candidate WP_089136810.1 CES79_RS07645 bifunctional acetaldehyde-CoA/alcohol dehydrogenase

Query= CharProtDB::CH_007085
         (453 letters)



>NCBI__GCF_002217945.1:WP_089136810.1
          Length = 873

 Score =  298 bits (762), Expect = 6e-85
 Identities = 169/435 (38%), Positives = 250/435 (57%), Gaps = 6/435 (1%)

Query: 7   IKELIEKAKVAQKKLEAYSQEQVDVLVKALGKVVYDNAEMFAKEAVEETEMGVYEDKVAK 66
           I  L+ KA  A   ++ ++QE+VD +V  +     D     AK AV+ET  GV+EDK  K
Sbjct: 24  IDALVNKAHDALCGMDDFTQEKVDHIVHQMAIAGLDQHMRLAKLAVDETGRGVWEDKAIK 83

Query: 67  CHLKSGAIWNHIKDKKTVGIIKEEPERALVYVAKPKGVVAATTPITNPVVTPMCNAMAAI 126
               +  IW+ IK+ KTVGII+++ ER L+ VA+P G++A  TP+TNP  T M  ++ A+
Sbjct: 84  NMFATEEIWHSIKNDKTVGIIEDDKERQLIKVAEPLGILAGVTPVTNPTSTTMFKSLIAV 143

Query: 127 KGRNTIIVAPHPKAKKVSAHTVELMNAELKKLGAPENIIQIVEAPSREAAKELMESADV- 185
           K RN II   HP+A+K S    ++M       GAPE +IQ +E PS EA   LM    V 
Sbjct: 144 KTRNPIIFGFHPQAQKSSVAAAKVMRDAAIAAGAPEGVIQWIEEPSLEATTALMNHPKVA 203

Query: 186 -VIATGGAGRVKAAYSSGRPAYGVGPGNSQVIVDKGYDYNKAAQDIITGRKYDNGIICSS 244
            V+ATGG G VKAAYS+G+PA GVGPGN    ++K  +  +A  DI+  + +DNG+IC++
Sbjct: 204 SVLATGGPGMVKAAYSTGKPALGVGPGNGPAYIEKTANIKRAVNDIVLSKTFDNGMICAT 263

Query: 245 EQSVIAPAEDYDKVIAAFVENGAFYVEDEETVEKFRSTLF--KDGKINSKIIGKSVQIIA 302
           E SVI  A+ Y+ V         F+++  +  +     ++  K G +   I G +   IA
Sbjct: 264 ENSVIIDADIYNDVKQEMKARKVFFIKKADQ-KALADAMYDPKRGSVKGPIAGMAAVKIA 322

Query: 303 DLAGVKVPEGTKVIVLKGKGAGEKDVLCKEKMCPVLVALKYDTFEEAVEIAMANYMYEGA 362
            LAG+ VPE TKV+  +    G  ++L  EK+CPV+   K    +E  +IA     + G 
Sbjct: 323 KLAGIDVPEDTKVLAAELTTVGPDNMLSAEKLCPVISVYKSADHKEGFKIANDLLHFGGL 382

Query: 363 GHTAGIHSDNDENIRYAGTVLPISRLVVNQPATTAG-GSFNNGFNPTTTLGCGSWGRNSI 421
           GHTA IH+++++     G  +  SR++VN P+   G G+  N   P+ TLG GSWG+NS+
Sbjct: 383 GHTAAIHTEDEDLATEYGIKMKASRVLVNTPSALGGIGNLYNEMIPSLTLGTGSWGKNSV 442

Query: 422 SENLTYEHLINVSRI 436
           S N++   L+N+  I
Sbjct: 443 SHNVSSFDLLNIKTI 457


Lambda     K      H
   0.313    0.131    0.368 

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: 966
Number of extensions: 41
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: 453
Length of database: 873
Length adjustment: 38
Effective length of query: 415
Effective length of database: 835
Effective search space:   346525
Effective search space used:   346525
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 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