GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bgtB' in Synechococcus elongatus PCC 7942

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine

Query= uniprot:Q31RP0
         (377 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0247 Synpcc7942_0247 ABC-type
           permease for basic amino acids and glutamine
          Length = 377

 Score =  750 bits (1936), Expect = 0.0
 Identities = 377/377 (100%), Positives = 377/377 (100%)

Query: 1   MPFRLKLQGPFWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQS 60
           MPFRLKLQGPFWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQS
Sbjct: 1   MPFRLKLQGPFWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQS 60

Query: 61  AGFNIGESAIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQ 120
           AGFNIGESAIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQ
Sbjct: 61  AGFNIGESAIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQ 120

Query: 121 LSRGYVAVVRNTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQTPGWL 180
           LSRGYVAVVRNTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQTPGWL
Sbjct: 121 LSRGYVAVVRNTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQTPGWL 180

Query: 181 VVILAIALVLFVSWLAQRQRSPRDWRWLYGAIAVVTVLMLLTQLSWPQQLQPGQIRGGLR 240
           VVILAIALVLFVSWLAQRQRSPRDWRWLYGAIAVVTVLMLLTQLSWPQQLQPGQIRGGLR
Sbjct: 181 VVILAIALVLFVSWLAQRQRSPRDWRWLYGAIAVVTVLMLLTQLSWPQQLQPGQIRGGLR 240

Query: 241 LSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALR 300
           LSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALR
Sbjct: 241 LSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALR 300

Query: 301 VIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVI 360
           VIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVI
Sbjct: 301 VIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVI 360

Query: 361 SAGMNGLQQRLQRWGVR 377
           SAGMNGLQQRLQRWGVR
Sbjct: 361 SAGMNGLQQRLQRWGVR 377


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: 721
Number of extensions: 29
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: 377
Length of database: 377
Length adjustment: 30
Effective length of query: 347
Effective length of database: 347
Effective search space:   120409
Effective search space used:   120409
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: 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