GapMind for catabolism of small carbon sources

 

Alignments for a candidate for x5p-reductase in Shewanella sp. ANA-3

Align Lmo2663 protein (characterized, see rationale)
to candidate 7026976 Shewana3_4105 L-threonine 3-dehydrogenase (RefSeq)

Query= uniprot:Q8Y414
         (343 letters)



>FitnessBrowser__ANA3:7026976
          Length = 341

 Score =  152 bits (385), Expect = 9e-42
 Identities = 106/333 (31%), Positives = 178/333 (53%), Gaps = 16/333 (4%)

Query: 16  LKDVEEPQVYGDKVKIKVAFTGICGSDIHTFK-GEYKNPTTPVTL--GHEFSGVVVEVGP 72
           L D  +P++  + + IK+  T ICG+D+H +   E+   T PV +  GHE+ G VV++G 
Sbjct: 15  LVDAPKPEMGHNDLLIKIKKTAICGTDMHIYNWDEWSQKTIPVPMVVGHEYVGEVVDIGQ 74

Query: 73  DVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQANGSFAEFVLSREESCH 132
           +V   K+GDRV+ E    TCG C  C+    +LC N  G+G    GSFAE+++    +  
Sbjct: 75  EVRGFKIGDRVSGEGHI-TCGHCRNCRAGRTHLCRNTSGVGVNREGSFAEYLVIPAFNAF 133

Query: 133 VLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGPIGLLLAQVVKAQGATVI 192
            + + IS + A++ +P    VH+AL    +  D  VL+ G GPIG++ A V +  GA  +
Sbjct: 134 KIPDDISDDLASIFDPFGNAVHTALSFDLVGED--VLITGAGPIGIMAAAVCRHVGARHV 191

Query: 193 MAGITKDSD-RLRLAKELGMDRIVDTLKEDLAEVV--LGMTGGYGAERVFDCSGAVPAVN 249
           +  IT  ++ RL LA+++G  R V+  +E L +V+  LGMT G+      + SG   A +
Sbjct: 192 V--ITDVNEYRLELARKMGATRAVNVAQESLKDVMKELGMTEGFDVG--LEMSGVPSAFH 247

Query: 250 QGLPLTKKKGDFVQVGLFAEKKNAIDEESIIQREIAYIGSRSQKP-SSWILALDLLANGK 308
             L      G    +G+    + AID   +I + +   G   ++   +W     L+ +G 
Sbjct: 248 AMLDTMNHGGKIAMLGI-PGGEMAIDWSKVIFKGLVIKGIYGREMFETWYKMASLIQSG- 305

Query: 309 IDTDKMITKVYGLDDWREAFEAVMAGNEIKVLV 341
           +D   +IT  Y +DD+++ F+A+ +G   KV++
Sbjct: 306 LDISPIITHHYKIDDFQKGFDAMGSGQSGKVIL 338


Lambda     K      H
   0.317    0.135    0.392 

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: 297
Number of extensions: 19
Number of successful extensions: 5
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: 343
Length of database: 341
Length adjustment: 29
Effective length of query: 314
Effective length of database: 312
Effective search space:    97968
Effective search space used:    97968
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 (21.6 bits)
S2: 49 (23.5 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