GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_3265
          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:

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