GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS24015 in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter related (characterized, see rationale)
to candidate Pf6N2E2_1800 putative ABC transporter ATP-binding protein

Query= uniprot:B2TBJ9
         (263 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1800 putative ABC
           transporter ATP-binding protein
          Length = 254

 Score =  266 bits (680), Expect = 3e-76
 Identities = 138/244 (56%), Positives = 180/244 (73%), Gaps = 1/244 (0%)

Query: 13  NIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLAGEEL 72
           +++K +   H LK I+++  QG+V+ I+G SGSGKST LRC+N LE  D G + + GE +
Sbjct: 9   SLNKYYDQFHALKDINIEVEQGEVLCIIGPSGSGKSTLLRCVNQLEKIDKGGLWVDGELV 68

Query: 73  KMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSRAESV 132
             +  G+ KL   +  Q+ R R   GMVFQ FNL+ HMTVL+N+IEGP +V KRS  E+ 
Sbjct: 69  GYRIVGN-KLHELNETQIARQRLSTGMVFQRFNLFPHMTVLQNIIEGPCQVLKRSPKEAN 127

Query: 133 EEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPELVGE 192
           EEA  LLA+VGLA+KR  YP  LSGGQQQRVAIARALAM PK+MLFDEPTSALDPELVGE
Sbjct: 128 EEALELLARVGLADKRNSYPIELSGGQQQRVAIARALAMRPKLMLFDEPTSALDPELVGE 187

Query: 193 VLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSDRFRQ 252
           VL VMR LA+ G TM+VVTHE+GFAR VSNR++F+  GQ+   G+P+E+ +  ++ R + 
Sbjct: 188 VLSVMRDLAQTGMTMIVVTHELGFAREVSNRMVFMDGGQIVEAGSPEEILISPQNPRTQS 247

Query: 253 FVSS 256
           F+S+
Sbjct: 248 FISA 251


Lambda     K      H
   0.318    0.133    0.377 

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: 179
Number of extensions: 5
Number of successful extensions: 2
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: 263
Length of database: 254
Length adjustment: 24
Effective length of query: 239
Effective length of database: 230
Effective search space:    54970
Effective search space used:    54970
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: 47 (22.7 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 paper from 2022 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