GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpD in Stenotrophomonas chelatiphaga DSM 21508

Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate WP_083491969.1 ABB28_RS07835 glycerol-3-phosphate dehydrogenase

Query= CharProtDB::CH_091834
         (512 letters)



>NCBI__GCF_001431535.1:WP_083491969.1
          Length = 501

 Score =  500 bits (1287), Expect = e-146
 Identities = 262/491 (53%), Positives = 327/491 (66%), Gaps = 9/491 (1%)

Query: 16  DVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFRLV 75
           DV VVGGGING GIA DAAGR L+V LCEQHDLA HTSSASSKL+HGGLRYLEH +F +V
Sbjct: 3   DVLVVGGGINGTGIARDAAGRVLTVALCEQHDLASHTSSASSKLVHGGLRYLEHGQFGMV 62

Query: 76  REALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKRE-KLPASRGL 134
           R++L ER VL+  APH+V+PL FVLPH  HLRPAW+I  GL+LYDHLG R  +LP SR L
Sbjct: 63  RKSLQERAVLMRIAPHLVQPLPFVLPHEAHLRPAWLIHLGLWLYDHLGGRSPQLPRSRSL 122

Query: 135 RFTG---SSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRSKG 191
           R  G    +PL+ ++RRGF Y+D    DARLVV+NAI A E GAH+ TRT C  A R   
Sbjct: 123 RLRGHPLGAPLREDLRRGFTYTDAQAPDARLVVVNAIDAAERGAHIWTRTVCEQAWRQAD 182

Query: 192 LWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPKLYE 251
            W + L   DG+  S+R R LVNA G W  RF+ +++       +RL+QGSHI+VP LY 
Sbjct: 183 GWSVDLRDPDGTQRSVRTRMLVNATGAWAPRFV-ENISLTRGVALRLVQGSHIVVPALYA 241

Query: 252 GEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNAHFK 311
            +HAY+LQ  D RIVFA+P+ D +T+IGTTD +++GDP  V + + +  YL    N  F+
Sbjct: 242 HDHAYLLQQPDGRIVFALPFEDHYTLIGTTDVDFEGDPGAVHVDDAQRDYLCAAANRSFR 301

Query: 312 QQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTYRKL 371
           QQ +  DI+  F+GVR L DD   E SA+TRDY L L A     PLL+V GGKLTTYR+L
Sbjct: 302 QQTSPRDIVWEFSGVRALLDDPEAEASAVTRDYRLDLDAEGA--PLLNVLGGKLTTYRRL 359

Query: 372 AESALTQLQPFFANLGPAWTAK-APLPGGEQMQSVEALTEQLANRYAWLDRELALRWART 430
           AE A+  L        PAWTA  A LPG E+    +     LA ++ WL  +LA RW+RT
Sbjct: 360 AEEAVDLLAGHAGTAAPAWTATGAQLPGAERGTPAQC-AAWLATQWPWLPPKLAARWSRT 418

Query: 431 YGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSKLGLFLSPS 490
           YG R   +L   +  A LG H G  LY  EV YLC HEWA+ A+D+LWRR++LGL L  +
Sbjct: 419 YGARATLILGQADSLAALGTHFGADLYEAEVRYLCTHEWARQADDVLWRRTRLGLVLDAA 478

Query: 491 QQVRLGQYLQS 501
           QQ RL  +L +
Sbjct: 479 QQHRLACWLDT 489


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: 781
Number of extensions: 32
Number of successful extensions: 5
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: 501
Length adjustment: 34
Effective length of query: 478
Effective length of database: 467
Effective search space:   223226
Effective search space used:   223226
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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