GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Marinicella litoralis KMM 3900

Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate WP_099019607.1 CCS90_RS11000 L-threonine 3-dehydrogenase

Query= SwissProt::Q8U259
         (348 letters)



>NCBI__GCF_002591915.1:WP_099019607.1
          Length = 340

 Score =  286 bits (733), Expect = 4e-82
 Identities = 146/342 (42%), Positives = 220/342 (64%), Gaps = 8/342 (2%)

Query: 5   MVAIMKTKPEYGAELVEVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIRPPQI 64
           M A++K KPE G  + +V +P+ G  +VLIKI  T+ICGTDLHIY+W+EW+   I+PP +
Sbjct: 1   MKALVKKKPELGIWMEDVPMPEMGHNDVLIKIEKTAICGTDLHIYKWDEWSAKAIKPPLV 60

Query: 65  MGHEVAGEVVEVGPGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGV 124
           +GHE  G +V++G  V+G EVG  VS E HIVCG C  C+ G  H+C NT+  GV+ +G 
Sbjct: 61  IGHEFVGHIVDMGSEVKGYEVGQRVSAEGHIVCGVCRNCRAGTPHLCPNTQGIGVNRNGA 120

Query: 125 FAEYAVVPAQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPIAGKSVLITGAGPLGLLGI 184
           FAE+  +P QN+W  P  IP   A   +P GNA    L   + G+ VLITGAGP+G++  
Sbjct: 121 FAEFISMPVQNLWPVPDKIPSNLAAFFDPFGNAAHCALEYDMVGEDVLITGAGPIGIIAT 180

Query: 185 AVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDV--VKEVMDITDGNGVDVFLE 242
            + K  GA  V++++ +++R +LAK +GA   +N  +E +  V + M+IT   G D+ +E
Sbjct: 181 GICKHVGARNVVITDVNDYRLSLAKDMGATRCVNVTKEKLPAVMKEMNIT---GFDLGME 237

Query: 243 FSGAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVYGITGRHLWETWYT 302
            SG P A    L ++   G+++LLG+ P    I+++N IIFK L++ GITGR ++ETWY 
Sbjct: 238 MSGNPMAFNDMLNSMYNGGKITLLGMLPDHTQINWDN-IIFKGLSIRGITGRKMYETWYK 296

Query: 303 VSRLLQSGKLNIDPIITHKYKGFDKYEEAFELMRAGKTGKVV 344
           +++LL SG   ++  +TH+    D ++  F+LM +G+ GKVV
Sbjct: 297 MTQLLLSG-FPLEKALTHEIH-IDDFQTGFDLMNSGQCGKVV 336


Lambda     K      H
   0.318    0.138    0.417 

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: 338
Number of extensions: 20
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: 348
Length of database: 340
Length adjustment: 29
Effective length of query: 319
Effective length of database: 311
Effective search space:    99209
Effective search space used:    99209
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: 49 (23.5 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