GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1732 Aerobic
           glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
          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 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