GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Alkalitalea saponilacus SC/BZ-SP2

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_079558920.1 CDL62_RS14220 L-threonine 3-dehydrogenase

Query= CharProtDB::CH_000596
         (353 letters)



>NCBI__GCF_002201795.1:WP_079558920.1
          Length = 340

 Score =  160 bits (405), Expect = 5e-44
 Identities = 103/332 (31%), Positives = 167/332 (50%), Gaps = 9/332 (2%)

Query: 20  IKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFILGHECAGEIAAV 79
           I ++ +PVP+  H++VLIK+    ICG+DLH Y         ++ P  +GHE  G +A  
Sbjct: 13  IWMQEIPVPEPGHNDVLIKITKTSICGTDLHIYNWDEWAQNNIKTPMTIGHEYVGYVAKK 72

Query: 80  GSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDGAFVQYIKMRQDF 139
           GS V   K GDRV  E  + C  C  C+ GR ++C     +    ++GAF  Y+ +  + 
Sbjct: 73  GSEVKNVKEGDRVTGEGHIACEHCRNCRRGRQHICEKTIGIGV-NINGAFADYVLVPSNN 131

Query: 140 VFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVGLMAVAAAKAFGAGT 199
           V  I   +  E  ++++PF    H A    L  G  + + G G +G M VA AK  GA  
Sbjct: 132 VMKISSKIPDEIVSIMDPFGNATHTALSFPL-IGEDVLVTGAGLIGSMCVAVAKFAGARY 190

Query: 200 IIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRGVDVAWETAGNPAALQSAL 259
           ++ T+L   R   AKKMGAT +IN +E++  + IK +    G D+  E +G+ AA    L
Sbjct: 191 VVATELNGYRASLAKKMGATKVINPKEENLSDVIKEL-GMIGFDIGLECSGSTAAFNQML 249

Query: 260 ASVRRGGKLAIVG-LPSQNEIPLNVPFIADNEI-DIYGIFRYANTYPKGIEFLASGIVDT 317
             +   GK+A++G LP++  +  N        +  IYG   +   Y    + L SG+ D 
Sbjct: 250 DHMYNSGKIALLGILPAKTMVDWNKMIFKGLTLKGIYGREMFETWYHME-QMLMSGL-DI 307

Query: 318 KHLVTDQYSLEQTQDAMERALQFKNECLKVMV 349
             L+T ++++++ Q   +  +     C KV++
Sbjct: 308 SPLITHRFNIDEYQKGFD--IMQTGNCGKVIL 337


Lambda     K      H
   0.320    0.137    0.401 

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: 288
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: 353
Length of database: 340
Length adjustment: 29
Effective length of query: 324
Effective length of database: 311
Effective search space:   100764
Effective search space used:   100764
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: 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