GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpD in Pseudomonas fluorescens FW300-N2C3

Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate AO356_18235 AO356_18235 glycerol-3-phosphate dehydrogenase

Query= CharProtDB::CH_091834
         (512 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_18235
          Length = 512

 Score =  792 bits (2045), Expect = 0.0
 Identities = 382/512 (74%), Positives = 442/512 (86%)

Query: 1   MSQAHTPSAPLAEVYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLI 60
           M  +  P+ PLAE+YDVAV+GGGINGVGIAADAAGRGLSVFLCE+ DLA HTSSASSKLI
Sbjct: 1   MPTSTLPTPPLAEIYDVAVIGGGINGVGIAADAAGRGLSVFLCEKDDLASHTSSASSKLI 60

Query: 61  HGGLRYLEHYEFRLVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYD 120
           HGGLRYLEHYEFRLVREALAEREVLL KAPHIVK +RFVLPHRPHLRPAWMIRAGLFLYD
Sbjct: 61  HGGLRYLEHYEFRLVREALAEREVLLTKAPHIVKQMRFVLPHRPHLRPAWMIRAGLFLYD 120

Query: 121 HLGKREKLPASRGLRFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTR 180
           HLGKRE+L  S+ L+F   +PLK+EI +GFEYSDC VDDARLVVLNA++ARE GAHVHTR
Sbjct: 121 HLGKREQLAGSKSLKFGADNPLKSEITKGFEYSDCWVDDARLVVLNAMAAREKGAHVHTR 180

Query: 181 TRCVSARRSKGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQ 240
           TRCV+ARRSKGLWHLHLER+DGSL+SIRA+ALVNAAGPWVA+FI+DDLK +SPYGIRLIQ
Sbjct: 181 TRCVNARRSKGLWHLHLERADGSLFSIRAKALVNAAGPWVAKFIRDDLKLESPYGIRLIQ 240

Query: 241 GSHIIVPKLYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETA 300
           GSH+IVPKLYEGEHA+ILQNED+RIVF IPYL++FT+IGTTDREY GDPAKVAI+E ET 
Sbjct: 241 GSHLIVPKLYEGEHAHILQNEDQRIVFTIPYLNQFTLIGTTDREYTGDPAKVAITEGETD 300

Query: 301 YLLQVVNAHFKQQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSV 360
           YLL+VVNAHFK+Q++  DILHS++GVRPLC+DESD PSA+TRDYTL+LS G  E PLLSV
Sbjct: 301 YLLKVVNAHFKKQISRDDILHSYSGVRPLCNDESDNPSAVTRDYTLALSGGGEEAPLLSV 360

Query: 361 FGGKLTTYRKLAESALTQLQPFFANLGPAWTAKAPLPGGEQMQSVEALTEQLANRYAWLD 420
           FGGKLTTYRKLAESA+ QL P+F  +  +WTA   LPGGE M + +AL   L +++ WL 
Sbjct: 361 FGGKLTTYRKLAESAMAQLAPYFTQMRGSWTAVEALPGGENMTTPQALCSALRDKFDWLP 420

Query: 421 RELALRWARTYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRR 480
            ++A RWA TYG+R WR+L+GV+   DLGEHLG GLY REVDYLC  EWA DA+DILWRR
Sbjct: 421 TDIARRWATTYGSRTWRMLEGVHDLGDLGEHLGAGLYTREVDYLCSDEWAIDAQDILWRR 480

Query: 481 SKLGLFLSPSQQVRLGQYLQSEHPHRPRVHAA 512
           SKLGLF +P++Q +L QYL     +R ++ AA
Sbjct: 481 SKLGLFTTPAEQEKLQQYLDKVEHNRRKIEAA 512


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: 930
Number of extensions: 30
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: 512
Length adjustment: 35
Effective length of query: 477
Effective length of database: 477
Effective search space:   227529
Effective search space used:   227529
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