GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpD in Pseudomonas fluorescens GW456-L13

Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate PfGW456L13_1732 Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)

Query= CharProtDB::CH_091834
         (512 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1732
          Length = 528

 Score =  782 bits (2020), Expect = 0.0
 Identities = 376/512 (73%), Positives = 441/512 (86%)

Query: 1   MSQAHTPSAPLAEVYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLI 60
           M  +  P+ PLAEVYD+AV+GGGINGVGIAADAAGRGLSVFLCE+ DLA HTSSASSKLI
Sbjct: 17  MPTSTLPTPPLAEVYDIAVIGGGINGVGIAADAAGRGLSVFLCEKDDLASHTSSASSKLI 76

Query: 61  HGGLRYLEHYEFRLVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYD 120
           HGGLRYLEHYEFRLVREALAEREVLLAKAPHIVK +RFVLPHRPHLRPAWMIRAGLFLYD
Sbjct: 77  HGGLRYLEHYEFRLVREALAEREVLLAKAPHIVKQMRFVLPHRPHLRPAWMIRAGLFLYD 136

Query: 121 HLGKREKLPASRGLRFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTR 180
           +LGKRE+L  S+ L+F   S LK+EI +GFEYSDC VDDARLVVLNA++ARE GAHVHT+
Sbjct: 137 NLGKREQLQGSKSLKFGPDSALKSEITKGFEYSDCWVDDARLVVLNAMAAREKGAHVHTQ 196

Query: 181 TRCVSARRSKGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQ 240
           TRCVSARR+KGLWHLHLER+DGSL+SIRA+ALVNAAGPWVARFI+DDLK +SPYGIRLIQ
Sbjct: 197 TRCVSARRTKGLWHLHLERADGSLFSIRAKALVNAAGPWVARFIRDDLKMESPYGIRLIQ 256

Query: 241 GSHIIVPKLYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETA 300
           GSH+IVPKLYEGEHA+ILQNED+RIVF IPYL+ FT+IGTTDREY GDPAKVAI++ ET 
Sbjct: 257 GSHLIVPKLYEGEHAHILQNEDQRIVFTIPYLNHFTLIGTTDREYTGDPAKVAITDGETD 316

Query: 301 YLLQVVNAHFKQQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSV 360
           YLL VVNAHFK+Q++  DILHS++GVRPLC+DESD PSA+TRDYTL+LS    E PLLSV
Sbjct: 317 YLLNVVNAHFKKQISREDILHSYSGVRPLCNDESDNPSAVTRDYTLALSGTGEEAPLLSV 376

Query: 361 FGGKLTTYRKLAESALTQLQPFFANLGPAWTAKAPLPGGEQMQSVEALTEQLANRYAWLD 420
           FGGKLTTYRKLAESAL QL P+F ++ P+WTA A LPGGE M + +AL+ ++ +++ W+ 
Sbjct: 377 FGGKLTTYRKLAESALAQLAPYFKHIQPSWTASATLPGGEDMTTPQALSSRIRDKFDWVP 436

Query: 421 RELALRWARTYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRR 480
            ++A RWA +YG+R WR+L+GV   +D+GEH+GGGLY REVDYLC  EWA  A DILWRR
Sbjct: 437 SDIARRWATSYGSRTWRMLEGVQDLSDMGEHIGGGLYTREVDYLCSEEWATTAHDILWRR 496

Query: 481 SKLGLFLSPSQQVRLGQYLQSEHPHRPRVHAA 512
           SKLGLF + ++Q +L  YL     +R ++ AA
Sbjct: 497 SKLGLFTTAAEQEKLKDYLNKIEQNRNKIEAA 528


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: 932
Number of extensions: 28
Number of successful extensions: 1
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: 528
Length adjustment: 35
Effective length of query: 477
Effective length of database: 493
Effective search space:   235161
Effective search space used:   235161
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: 52 (24.6 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