GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gatY in Shewanella loihica PV-4

Align D-tagatose-1,6-bisphosphate aldolase subunit KbaY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Ketose 1,6-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate 5208243 Shew_0755 fructose-1,6-bisphosphate aldolase (RefSeq)

Query= SwissProt::Q9KIP8
         (286 letters)



>FitnessBrowser__PV4:5208243
          Length = 354

 Score =  174 bits (442), Expect = 2e-48
 Identities = 112/326 (34%), Positives = 172/326 (52%), Gaps = 45/326 (13%)

Query: 1   MSIISTKYLLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGTFKHIALE 60
           M++IS + LL  A  +GY VPAFN++N E ++AI++      SPVI+  + G  K+   +
Sbjct: 1   MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQ 60

Query: 61  EI-YALCSAYSTTYNMPLALHLDHHESLDDIRRKVHAGVRSAMIDGSHFP-------FAE 112
            + Y + +A     ++P+ +H DH    D  +R +  G+ S M+DGS          +  
Sbjct: 61  FLKYLMAAALEQYPDIPVCIHQDHGTHPDVCQRSIQLGMSSVMMDGSLMSDGKTPASYEY 120

Query: 113 NVKLVKSVVDFCHSQDCSVEAELGRLG-------GVEDDMSVD---AESAFLTDPQEAKR 162
           NV + +  V F H+   SVE E+G LG       G ED +  +   +E   LT P+EA R
Sbjct: 121 NVDVTRKTVAFAHACGVSVEGEIGCLGSLETGQAGEEDGVGAEGILSEDQLLTTPEEAAR 180

Query: 163 FVELTGVDSLAVAIGTAHGLY--SKTPKIDFQRLAEIREV----VDVPLVLHGASDVPDE 216
           FV  T VD+LA+AIGT+HG Y  S+ P  D  R+  I+E+     +  LV+HG+S VP E
Sbjct: 181 FVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQE 240

Query: 217 FVR---------------------RTIELGVTKVNVATELKIAFAGAVKAWFAENPQGND 255
           ++                        I+ GV KVN+ T+L++A  GAV+ + AENP   D
Sbjct: 241 WLEVINQYGGAIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKFLAENPSEFD 300

Query: 256 PRNYMRVGMDAMKEVVRNKINVCGSA 281
           PR +++  MDAM ++   +    G+A
Sbjct: 301 PRKFLKASMDAMADICTVRYEAFGAA 326


Lambda     K      H
   0.319    0.133    0.384 

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: 247
Number of extensions: 11
Number of successful extensions: 7
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: 286
Length of database: 354
Length adjustment: 27
Effective length of query: 259
Effective length of database: 327
Effective search space:    84693
Effective search space used:    84693
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: 48 (23.1 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