GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB' in Pseudomonas fluorescens FW300-N2E2

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate Pf6N2E2_4281 Amino acid ABC transporter, permease protein

Query= uniprot:Q31RP0
         (377 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4281
          Length = 265

 Score = 81.3 bits (199), Expect = 3e-20
 Identities = 53/159 (33%), Positives = 87/159 (54%), Gaps = 17/159 (10%)

Query: 217 VLMLLTQLSWPQQ-LQPGQIRGGL-RLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAG 274
           + +LL  L  PQ  + PG I  G+  LSL +           GA+++EI R GIL VP G
Sbjct: 112 IQILLIYLGLPQLGVVPGAIAAGIIALSLNY-----------GAYLSEIFRAGILGVPHG 160

Query: 275 QWEAAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQT 334
           Q EA+ ALGL+ +   W++ +PQA+R I+P   +Q++   K+SSL   +G  ++   AQ+
Sbjct: 161 QREASLALGLSETVIFWRVTLPQAMRTIIPPTTNQFISMLKDSSLISVMGVWEVMFLAQS 220

Query: 335 TLNQTGRPVEVFLILMLTYLAINAVISAGMNGLQQRLQR 373
                GR    ++ ++ T   I  ++S  +  +Q R++R
Sbjct: 221 ----YGRSSYRYIEMLTTAAIIYWLMSIALELIQARMER 255



 Score = 31.2 bits (69), Expect = 3e-05
 Identities = 18/70 (25%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 85  GLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVWY-- 142
           G V +L +    ++ ++++G +  +A  S + +   ++  Y +  R TPLL+Q+++ Y  
Sbjct: 61  GAVLTLFLCLCSIVASSLLGFITALARLSSSAVAFGIASFYASFFRGTPLLIQILLIYLG 120

Query: 143 FPILLSLPAA 152
            P L  +P A
Sbjct: 121 LPQLGVVPGA 130


Lambda     K      H
   0.326    0.140    0.445 

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: 240
Number of extensions: 7
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 377
Length of database: 265
Length adjustment: 27
Effective length of query: 350
Effective length of database: 238
Effective search space:    83300
Effective search space used:    83300
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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