GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Paraburkholderia bryophila 376MFSha3.1

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate H281DRAFT_03586 H281DRAFT_03586 L-threonine 3-dehydrogenase

Query= CharProtDB::CH_000596
         (353 letters)



>FitnessBrowser__Burk376:H281DRAFT_03586
          Length = 343

 Score =  182 bits (462), Expect = 1e-50
 Identities = 110/333 (33%), Positives = 174/333 (52%), Gaps = 7/333 (2%)

Query: 9   MKA-AVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFI 67
           MKA A +     + +  + VP++ H++V+I++    ICG+D+H +         +  P  
Sbjct: 1   MKALAKLERAPGLTLTDVKVPEVGHNDVMIRIKRTAICGTDIHIWKWDDWAQKTIPVPMH 60

Query: 68  LGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDG 127
           +GHE  GEI  +G+ V  F +GDRV+ E  +TCG C  C+ GR +LC +   +     +G
Sbjct: 61  VGHEYVGEIVEMGAEVRGFSIGDRVSGEGHITCGFCRNCRAGRRHLCRNTVGVGVNR-EG 119

Query: 128 AFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVGLM 187
           AF +Y+ +     F IP  +S + AA+ +PF    H A    L  G  + I G GP+G+M
Sbjct: 120 AFAEYLVIPAFNAFKIPPEISDDLAAIFDPFGNATHTALSFNLV-GEDVLITGAGPIGIM 178

Query: 188 AVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRGVDVAWE 247
           AVA AK  GA  +++TD+   RL  A+KMGAT  +N+  +   + +  +    G DV  E
Sbjct: 179 AVAIAKHVGARNVVITDINDYRLGLARKMGATRAVNVSRESLRDVMADLHMAEGFDVGLE 238

Query: 248 TAGNPAALQSALASVRRGGKLAIVGL-PSQNEIPLNVPFIADNEI-DIYGIFRYANTYPK 305
            +G P A    L ++  GGK+A++G+ P+Q  I  N       EI  IYG   +  T+ K
Sbjct: 239 MSGVPGAFTGMLEAMNHGGKIALLGIPPAQTAIDWNQVIFKGLEIKGIYGREMF-ETWYK 297

Query: 306 GIEFLASGIVDTKHLVTDQYSLEQTQDAMERAL 338
            +  L SG+ D   ++T  + ++  Q A    L
Sbjct: 298 MVAMLQSGL-DLSPILTHHFKVDDYQQAFATML 329


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: 283
Number of extensions: 16
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: 353
Length of database: 343
Length adjustment: 29
Effective length of query: 324
Effective length of database: 314
Effective search space:   101736
Effective search space used:   101736
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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