GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glk in Bacteroides thetaiotaomicron VPI-5482

Align General specificity hexokinase (characterized, see rationale)
to candidate 351958 BT2430 hexokinase type III (NCBI ptt file)

Query= uniprot:Q5GAN8
         (402 letters)



>lcl|FitnessBrowser__Btheta:351958 BT2430 hexokinase type III (NCBI
           ptt file)
          Length = 402

 Score =  678 bits (1749), Expect = 0.0
 Identities = 332/402 (82%), Positives = 364/402 (90%)

Query: 1   MEKNIFKLDNEQLKGIAHAFREKVEEGLNKNNAEIQCIPTFILPKATDIKGKALVLDLGG 60
           MEKNIFKLDNEQLK I  +FR+K EEGL   NAEIQCIPTFI PK T IKGK+LVLDLGG
Sbjct: 1   MEKNIFKLDNEQLKAIVCSFRDKTEEGLKTENAEIQCIPTFIAPKTTHIKGKSLVLDLGG 60

Query: 61  TNYRVAIVDFSTEKPIIYPNNGWKKDMSIMKSPGYTREELFKELADLIVEIKREEEMPIG 120
           TNYRVAIVDF    P ++PNNGWKKDMSIMKS GYTREELFKELAD+I+ IKREEEMPIG
Sbjct: 61  TNYRVAIVDFDKATPTVHPNNGWKKDMSIMKSVGYTREELFKELADMIIGIKREEEMPIG 120

Query: 121 YCFSYPTESIPGGDARLLRWTKGVDIREMVGQFVGKPLLDYLNEKNKIRFTGVKVLNDTI 180
           YCFSYP ES+PGGDA+LLRWTKGVDI+EMVG+F+GKPLLDYLNE+NKI+FTG+KV+NDTI
Sbjct: 121 YCFSYPAESVPGGDAKLLRWTKGVDIKEMVGEFIGKPLLDYLNERNKIKFTGIKVVNDTI 180

Query: 181 ASLFAGLTDKSYDAYIGLIVGTGTNMATFIPSDKITKLDPECHVQGLIPVNLESGNFYPP 240
           ASLFAGLTD SYDAYIGLIVGTGTNMATFIP+DKI KLD  C+  GLIPVNLESGNF+PP
Sbjct: 181 ASLFAGLTDNSYDAYIGLIVGTGTNMATFIPADKIEKLDQSCNAHGLIPVNLESGNFHPP 240

Query: 241 FLTAVDDTVDATSDSLGKQRFEKAVSGMYLGDILKAAFPLEEFEEKFDARKLTAIMNYPD 300
           FLTAVDDTVDA S + GKQRFEKAVSGMYLGDILK AFPLEEFEEKFDA+KLT+IMNYPD
Sbjct: 241 FLTAVDDTVDAISGNPGKQRFEKAVSGMYLGDILKTAFPLEEFEEKFDAQKLTSIMNYPD 300

Query: 301 IHKDIYVQVAHWIYNRSAQLVAASLAGLIALLKSYNRDIHRVCLIAEGSLFWSESRKDKN 360
           I+KD+YVQVA WIY RSAQLVAASL GLI LLKSYN+DI +VCL+AEGSLFWSE+RKDKN
Sbjct: 301 IYKDVYVQVAQWIYGRSAQLVAASLTGLIMLLKSYNKDIRKVCLVAEGSLFWSENRKDKN 360

Query: 361 YNILVMEKLQELLRELELEDVEVHINSMDNANLIGTGIAALS 402
           YNILVMEKL+ELL+   LED+EV I SM+NANLIGTGIAALS
Sbjct: 361 YNILVMEKLRELLQLFGLEDIEVDIKSMNNANLIGTGIAALS 402


Lambda     K      H
   0.318    0.138    0.399 

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: 614
Number of extensions: 10
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: 402
Length of database: 402
Length adjustment: 31
Effective length of query: 371
Effective length of database: 371
Effective search space:   137641
Effective search space used:   137641
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 (21.7 bits)
S2: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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