GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Escherichia coli BW25113

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>FitnessBrowser__Keio:17511
          Length = 356

 Score =  190 bits (483), Expect = 4e-53
 Identities = 126/356 (35%), Positives = 193/356 (54%), Gaps = 12/356 (3%)

Query: 3   LALDSISKKVGAQTWLYD-MSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTV 61
           L L +++K    +T +   ++L +  G   V++G +  GK++L+R++AGL+  T G + +
Sbjct: 4   LKLQAVTKSWDGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGDIWI 63

Query: 62  DGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRLH 119
           + + VT M  +DR +AMV+Q +  YP M V  N+A  LK+RG  ++ I  RV+E A  L 
Sbjct: 64  NDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAARILE 123

Query: 120 IDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAA 179
           +D  L R P ELSGGQ+QRVA+ RA+ +   + L DEPL NLD KLR ++R EL QL   
Sbjct: 124 LDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQLHRR 183

Query: 180 GQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLM 239
            ++T +Y T +  EA+ L     V++ G   Q G   EV+  P SL VA     P MNL+
Sbjct: 184 LKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAMNLL 243

Query: 240 AASATAQGVRLQGGAELTLPLPQGAATAAG--LTVGVRASALRVHARPGDVSVAGVVELA 297
                 +G   +    + LPL  G    AG  +T+G+R   + + ++  +  V  V++  
Sbjct: 244 TGRVNNEGTHFELDGGIELPLNGGYRQYAGRKMTLGIRPEHIALSSQ-AEGGVPMVMDTL 302

Query: 298 EISGSDTFVHASTPWGD--LVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLAQ 351
           EI G+D   H    WG+  LV +L        G+ + LHL   Q ++F  DG   Q
Sbjct: 303 EILGADNLAHGR--WGEQKLVVRLAHQERPTAGSTLWLHLAENQLHLF--DGETGQ 354


Lambda     K      H
   0.318    0.133    0.375 

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: 272
Number of extensions: 16
Number of successful extensions: 3
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: 363
Length of database: 356
Length adjustment: 29
Effective length of query: 334
Effective length of database: 327
Effective search space:   109218
Effective search space used:   109218
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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