GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpT in Marinobacter adhaerens HP15

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF2209 HP15_2163 sugar ABC transporter, ATP-binding protein

Query= TCDB::G3LHY9
         (356 letters)



>lcl|FitnessBrowser__Marino:GFF2209 HP15_2163 sugar ABC transporter,
           ATP-binding protein
          Length = 366

 Score =  365 bits (937), Expect = e-105
 Identities = 190/364 (52%), Positives = 251/364 (68%), Gaps = 14/364 (3%)

Query: 1   MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60
           MA I L  + H+Y   P    DY+++++DH W+ GGAYALLGPSGCGK+T+LNIISGL+Q
Sbjct: 1   MAEIQLKSLAHSYSDMPTGPDDYAIRQLDHVWHKGGAYALLGPSGCGKSTMLNIISGLVQ 60

Query: 61  PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120
           PS G +LFDGK V  LS + RNIAQVFQFPVIYD+MTVYDNLAFPL+N  V  + +  RV
Sbjct: 61  PSEGDVLFDGKRVNELSPRDRNIAQVFQFPVIYDSMTVYDNLAFPLKNNKVPASKIKARV 120

Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180
            +I E++++     +KA+ LTAD+KQK+S+GRGLVR DV+AILFDEPLTVIDP +KW LR
Sbjct: 121 HEIAEVLEIEDKLYKKAKNLTADEKQKVSMGRGLVREDVSAILFDEPLTVIDPQLKWKLR 180

Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240
            +LK++H+QF  TMVYVTHDQ EA TFA+K+ VMY GQIVQ GTP ELFE+P+HTFVG+F
Sbjct: 181 RKLKQIHEQFDITMVYVTHDQLEASTFADKIAVMYGGQIVQFGTPTELFEQPNHTFVGFF 240

Query: 241 IGSPGMNFMPAR------IEGSTVKVGDETLTLEYAPKTSGTAKTELGIRPEFIRLGREG 294
           IGSPGMN +  +        GSTV V  E+  ++   +T  T   ++GIRPEF+ +    
Sbjct: 241 IGSPGMNLIEVQRCPRGVCFGSTV-VSLESWQVDVLQRTRST-NIKIGIRPEFVEVSSVA 298

Query: 295 MPIT----ISKVEDIGRQKIVRARFADQPIAIVVPED--ADIPADARVTFDPSAISIYAD 348
              T    +  VED+G  KIV  +   + + +   E+  A I +   ++F    + +Y D
Sbjct: 299 SDDTFEAEVLDVEDLGTYKIVTVQLDHEKMKVRQSEEFAASIGSKVHLSFPRQWLKLYVD 358

Query: 349 SWRV 352
            + V
Sbjct: 359 EFLV 362


Lambda     K      H
   0.321    0.137    0.405 

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: 390
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: 356
Length of database: 366
Length adjustment: 29
Effective length of query: 327
Effective length of database: 337
Effective search space:   110199
Effective search space used:   110199
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: 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 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