GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Marivita geojedonensis DPG-138

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_085639493.1 MGEO_RS14935 D-glycerate dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>NCBI__GCF_002115805.1:WP_085639493.1
          Length = 328

 Score =  259 bits (662), Expect = 6e-74
 Identities = 138/320 (43%), Positives = 207/320 (64%), Gaps = 7/320 (2%)

Query: 5   VFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELLEN 64
           V +TR++P+     +++ +++ L        +  L + V+E D LV  +TD++D  L+  
Sbjct: 8   VVVTRRLPDAVETRLKELFDVRLRDSDTPMTQAELTDAVKEADVLVPTLTDRIDAGLIGQ 67

Query: 65  A-PKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEAD 123
           A  +L++IA Y  G D+ID++ A  RGI V+NTPGV+T+ TAD+  AL+L+V RRI E  
Sbjct: 68  AGERLRLIANYGAGVDHIDVDTARSRGILVSNTPGVVTEDTADMVMALMLSVTRRIPEGL 127

Query: 124 AFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRTR 183
           + +++G+W     GW P  FLG  L G+ LGI+G GRIGQA+A+RAK FGM+I Y++R R
Sbjct: 128 SVMQTGDWD----GWAPTAFLGGRLGGRRLGILGMGRIGQAVARRAKAFGMQIHYHNRRR 183

Query: 184 -KPEAEEEIGAEYVD-FETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSR 241
            + E E+ + A Y +  + ++   D +S++ P T  T+H++  + LKL+KP+A+++NTSR
Sbjct: 184 LRSEIEDALEATYWESLDQMVARMDILSVNCPHTPSTFHLLNARRLKLLKPSAVIVNTSR 243

Query: 242 GAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGMA 301
           G V+D NAL + LK G +AGAGLDV+E     N EL  + NVV+ PH+GSAT E R  M 
Sbjct: 244 GEVIDENALTRMLKAGELAGAGLDVYEHGHRGNPELRNMPNVVMLPHMGSATQEGRLEMG 303

Query: 302 ELVAKNLIAFAKGEIPPNLV 321
           E V  N+  FA G  PP+ V
Sbjct: 304 EKVIINVKTFADGHRPPDQV 323


Lambda     K      H
   0.317    0.137    0.392 

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: 277
Number of extensions: 10
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: 331
Length of database: 328
Length adjustment: 28
Effective length of query: 303
Effective length of database: 300
Effective search space:    90900
Effective search space used:    90900
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 (21.6 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