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_01517 H281DRAFT_01517 L-idonate 5-dehydrogenase

Query= CharProtDB::CH_000596
         (353 letters)



>FitnessBrowser__Burk376:H281DRAFT_01517
          Length = 348

 Score =  209 bits (533), Expect = 7e-59
 Identities = 117/347 (33%), Positives = 191/347 (55%), Gaps = 12/347 (3%)

Query: 9   MKAAVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFIL 68
           M AAV+H  + I+I+ +  P+    +V ++V A GICGSDL YY  G+ G++ V +PF+L
Sbjct: 1   MLAAVLHEPKLIRIDEVAPPEPGPGQVRVRVRAGGICGSDLSYYFKGKSGDFAVREPFVL 60

Query: 69  GHECAGEIAAVGSSVD---QFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLAT--- 122
           GHE AGEI ++G  V    +   G RVAV PG+ CG C+ C  G  N C +++F+ +   
Sbjct: 61  GHEVAGEIDSLGEGVSADARLVPGQRVAVNPGLACGTCKYCTIGMPNHCLNMRFMGSAST 120

Query: 123 -PPVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGM 181
            P   G F QYI +       + DS+ + +A++ EP +V +HA  R     G+++ ++G 
Sbjct: 121 FPHTQGMFRQYIVVAARQCIPVADSVDFAQASMAEPLAVALHAVKRAGSLVGASVLLIGC 180

Query: 182 GPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRG 241
           GP+G + ++ A+  GA  ++  DL    L+ A ++GA   +N  +   +E+       RG
Sbjct: 181 GPIGCILLSVARRAGAHRVVAVDLSSRALQVAAQLGADQTVNAADSATIEQWSA---QRG 237

Query: 242 V-DVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIFRYA 300
             DV  E +G+PA L++AL S R GG +  VG     + P+    +   E+   G FR+ 
Sbjct: 238 TFDVVIEASGSPAGLETALRSARAGGTVIQVGNLPAGQSPVAANLVMSKELRYQGSFRFT 297

Query: 301 NTYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQFKNECLKV 347
           + Y    + +ASG VD + L+T  +++     A E AL  +++ +KV
Sbjct: 298 DEYAIAADEIASGKVDLRPLMTHAFAMSDANQAFEVALD-RSQSMKV 343


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: 272
Number of extensions: 17
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: 348
Length adjustment: 29
Effective length of query: 324
Effective length of database: 319
Effective search space:   103356
Effective search space used:   103356
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.

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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