GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Nocardiopsis gilva YIM 90087

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_094932730.1 CDO52_RS24225 phosphomannomutase/phosphoglucomutase

Query= BRENDA::Q8PGN7
         (450 letters)



>NCBI__GCF_002263495.1:WP_094932730.1
          Length = 454

 Score =  311 bits (797), Expect = 3e-89
 Identities = 184/441 (41%), Positives = 249/441 (56%), Gaps = 11/441 (2%)

Query: 8   FKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAGLRASG 67
           FKAYD+RG VPD L+ D++R IG A A  +    VV+ +D+R +SP L  A + G+   G
Sbjct: 8   FKAYDVRGVVPDTLDADISRAIGAAFARVVGGDAVVVAYDMRPSSPELATAFAEGVTGQG 67

Query: 68  RDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGLFAI 127
            DV+  GL  T+ +YF + +L    G M TASHNP  YNG+K+ + +A PISS+TGL  I
Sbjct: 68  LDVVFAGLGSTDLLYFASGHL-GLPGAMFTASHNPAQYNGIKMCKAEAAPISSETGLDEI 126

Query: 128 RDTVAADTAAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAGLIV-- 185
           R            PT S   R    AY  HL S VD + ++PLK+VV+AGNG  G  V  
Sbjct: 127 RTLAEKGVPPHDGPTGSITERDMLAAYAAHLRSLVDLTDVRPLKVVVDAGNGMGGHTVPA 186

Query: 186 ---DLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDGDF 242
              D +   LP E V +F E DG FPN   NPL P+N       V+  GAD G+A+DGD 
Sbjct: 187 VLGDTVLDPLPLEIVPLFFELDGTFPNHPANPLDPDNIVDLQDKVRATGADIGVAFDGDA 246

Query: 243 DRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVLCK 302
           DRCF  D  G  +    +  ++A   LAK+PG  ++H+   +    E V E GG PV  +
Sbjct: 247 DRCFVVDERGEPVPPSAITAMVAVRELAKEPGATIIHNLITSHAVPEIVRENGGEPVRTR 306

Query: 303 SGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLVEA 362
            GH+FIKE M    A++GGE SAH+YFR+F  AD+GM+  + +   +  S   L++ + A
Sbjct: 307 VGHSFIKETMAQTGAIFGGEHSAHYYFRDFWRADTGMLAAMHVLRFLGSSTGKLSE-ITA 365

Query: 363 RMQKFPCSGEINFKVADAKASVARVMEHYAS-LSPELDYTDGISADF--GQWRFNLRSSN 419
              ++  SGEIN +VADA   +A V   Y       +D  DG++     G W FNLR+SN
Sbjct: 366 EYSRYAASGEINSEVADASGRMAAVEAAYTGRADARIDDLDGLTVALADGSW-FNLRASN 424

Query: 420 TEPLLRLNVETRGDAALLETR 440
           TEPLLRLNVE      + + R
Sbjct: 425 TEPLLRLNVEAPDTETMAKLR 445


Lambda     K      H
   0.319    0.136    0.404 

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: 533
Number of extensions: 25
Number of successful extensions: 5
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: 450
Length of database: 454
Length adjustment: 33
Effective length of query: 417
Effective length of database: 421
Effective search space:   175557
Effective search space used:   175557
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 (21.7 bits)
S2: 51 (24.3 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