GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xdh in Sinorhizobium meliloti 1021

Align D-xylose dehydrogenase; NADP-dependent D-xylose dehydrogenase; EC 1.1.1.179 (characterized)
to candidate SMc04133 SMc04133 oxidoreductase

Query= SwissProt::Q8GAK6
         (388 letters)



>lcl|FitnessBrowser__Smeli:SMc04133 SMc04133 oxidoreductase
          Length = 382

 Score =  450 bits (1157), Expect = e-131
 Identities = 221/381 (58%), Positives = 275/381 (72%), Gaps = 5/381 (1%)

Query: 9   VAMNGITGRMGYRQHLLRSILPIRDAGGFTLEDGTKVQIEPILVGRNEAKIRELAEKHKV 68
           + ++G+TGRMGY QHL+RSIL IRD GG TL+ G +++I+PI+VGRN  K+ +LA++H +
Sbjct: 6   IILHGVTGRMGYNQHLVRSILAIRDRGGITLQSGERLEIDPIIVGRNRDKMEQLAKRHDI 65

Query: 69  AEWSTDLDSVVNDPTVDIIFDASMTSLRAATLKKAMLAGKHIFTEKPTAETLEEAIELAR 128
           A WSTDLD+ + DP   I FDA  T +RA  + +A+ AGKH++ EKP ++ L  A++LAR
Sbjct: 66  ARWSTDLDAALADPNDQIFFDAGTTLMRAELIGRALDAGKHVYCEKPISDDLRTAVKLAR 125

Query: 129 IGKQAGVTAGVVHDKLYLPGLVKLRRLVDEGFFGRILSIRGEFGYWVFEGDVQA-AQRPS 187
             + +G+  GVV DKL+LPGL KL  L D GFFG+ILS+RGEFGYWVFEGD    AQRPS
Sbjct: 126 KARASGLKHGVVQDKLFLPGLRKLALLRDSGFFGKILSVRGEFGYWVFEGDWGVPAQRPS 185

Query: 188 WNYRKEDGGGMTTDMFCHWNYVLEGIIGKVKSVNAKTATHIPTRWDEAGKEYKATADDAS 247
           WNYRK+DGGG+  DM CHW YVL+ + G+VK+V+   ATHIP+R DE G+ Y    DDA+
Sbjct: 186 WNYRKKDGGGIILDMLCHWRYVLDNLFGEVKAVSCLGATHIPSRIDEQGRAYDCDTDDAA 245

Query: 248 YGIFELETPGGDDVIGQINSSWAVRVYRDELVEFQVDGTHGSAVAGLNKCVAQQRAHTPK 307
           Y  FELE  GG  ++  INSSWAVRV RD+LV FQVDGTHGSAVAGL KC  Q R +TPK
Sbjct: 246 YATFELE--GG--IVAHINSSWAVRVRRDDLVTFQVDGTHGSAVAGLTKCWTQHRVNTPK 301

Query: 308 PVWNPDLPVTESFRDQWQEVPANAELDNGFKLQWEEFLRDVVAGREHRFGLLSAARGVQL 367
           PVWNPD P T  F   W EVP     DNGFK QWE FLR V        GL + A+GVQL
Sbjct: 302 PVWNPDQPQTIDFYRTWDEVPDTQAFDNGFKAQWEMFLRHVAEDGPWPHGLEAGAKGVQL 361

Query: 368 AELGLQSNDERRTIDIPEITL 388
           AELGL+S  ERR +D+PE+ L
Sbjct: 362 AELGLKSWAERRWLDVPELEL 382


Lambda     K      H
   0.318    0.136    0.406 

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: 561
Number of extensions: 20
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: 388
Length of database: 382
Length adjustment: 30
Effective length of query: 358
Effective length of database: 352
Effective search space:   126016
Effective search space used:   126016
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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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