GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMc04133
          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:

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