GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpD in Sphingomonas koreensis DSMZ 15582

Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate Ga0059261_3265 Ga0059261_3265 Glycerol-3-phosphate dehydrogenase

Query= CharProtDB::CH_091834
         (512 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_3265 Ga0059261_3265
           Glycerol-3-phosphate dehydrogenase
          Length = 377

 Score =  340 bits (873), Expect = 4e-98
 Identities = 197/386 (51%), Positives = 240/386 (62%), Gaps = 14/386 (3%)

Query: 15  YDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFRL 74
           YD+ + GGGING  IA +A+  GLSV L E+ DLA HTSSASSKLIHGGLRYLE YEFRL
Sbjct: 3   YDLLIAGGGINGCAIAREASLLGLSVLLVEKDDLAAHTSSASSKLIHGGLRYLETYEFRL 62

Query: 75  VREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKREKLPASRGL 134
           VREAL ERE +LA APH++ P+ FVLPH   +RP WM+RAGL+LYD LG    LP SR L
Sbjct: 63  VREALHERERMLAAAPHLIHPMAFVLPHAHSVRPWWMVRAGLYLYDLLGLGSSLPRSRAL 122

Query: 135 RFTGSSPLKAEIRR---GFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRSKG 191
           R     P  A I     GF Y D  VDDA LV  NA  A  +GA V T      A R   
Sbjct: 123 R--RDDPRLAPIAHNVGGFLYWDAQVDDAALVRANAADAVANGAQVETGVAVTGAERGGM 180

Query: 192 LWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPKLYE 251
            WH+ L        +I  RA+VNA GPWV  F+ D ++ ++  G+RLI+GSHI+VP L+E
Sbjct: 181 GWHVFL----SDRRTIDTRAIVNATGPWVKAFL-DTIRIRTTSGLRLIKGSHIVVPALWE 235

Query: 252 GEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNAHFK 311
           G+HAYILQ  DRR+VFA P+    TMIGTTD   +  P    I+  E  YL    N +F+
Sbjct: 236 GDHAYILQQPDRRVVFATPWRGG-TMIGTTDVPVE-RPEDAGITSAEIDYLCAAANRYFR 293

Query: 312 QQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTYRKL 371
           +Q+A AD+  +++G+R L DD  DE   ITRDY L L   +   P+LSVFGGK+TT R L
Sbjct: 294 RQIAPADVTGTWSGIRALYDDGKDEARTITRDYVLELDTSSA--PILSVFGGKITTARAL 351

Query: 372 AESALTQLQPFFANLGPAWTAKAPLP 397
            E AL +L P         T   PLP
Sbjct: 352 GEHALAKLAPALGFTARPVTRDRPLP 377


Lambda     K      H
   0.321    0.136    0.415 

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: 534
Number of extensions: 24
Number of successful extensions: 6
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: 512
Length of database: 377
Length adjustment: 32
Effective length of query: 480
Effective length of database: 345
Effective search space:   165600
Effective search space used:   165600
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: 51 (24.3 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