GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:351958
          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 (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