GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB' in Phaeobacter inhibens BS107

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate GFF2619 PGA1_c26600 amino acid ABC transporter, permease protein

Query= uniprot:Q31RP0
         (377 letters)



>FitnessBrowser__Phaeo:GFF2619
          Length = 273

 Score = 78.2 bits (191), Expect = 2e-19
 Identities = 58/202 (28%), Positives = 99/202 (49%), Gaps = 17/202 (8%)

Query: 184 LAIALVLFVSWLAQRQRSPRDWRWLYGAIAVVTVLMLLTQLSWPQQLQPGQIRGGL---- 239
           L +AL     WL  RQ +    R+    +  + +++LL  +++       ++R  L    
Sbjct: 72  LGLALAAGSRWLVIRQGA----RFYIEVVRGIPIIVLLLYVAFVLAPALVELRNWLGDHI 127

Query: 240 --------RLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLW 291
                      L + A++  ++AY+ AFI+E+ R G+ SV  GQ EAA +LGL+R     
Sbjct: 128 GLDPIRTRNFPLLWRAIIALMIAYS-AFISEVFRAGLQSVDEGQIEAAKSLGLSRWHRFR 186

Query: 292 QIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILML 351
            IV PQA+R I+P L + +V   K+SSL   +G  D+    + T     R  E + ++ L
Sbjct: 187 FIVFPQAIRTILPPLGNDFVALVKDSSLVSVLGVADVTQLGKLTAVGNFRYFETYNVVAL 246

Query: 352 TYLAINAVISAGMNGLQQRLQR 373
            YL +   +S  +   ++ L+R
Sbjct: 247 IYLTLTIGLSLLLRRFEKHLRR 268



 Score = 37.0 bits (84), Expect = 6e-07
 Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 3/84 (3%)

Query: 77  SYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLL 136
           S    L+ G+  ++ V  I   L +++G    +AA S   ++RQ +R Y+ VVR  P+++
Sbjct: 44  SILSTLMRGVQLTIFVTLISFFLASLLGLGLALAAGSRWLVIRQGARFYIEVVRGIPIIV 103

Query: 137 QLIVWYFPILLSLPAAQQPWHWLG 160
            L+  Y   +L+ PA  +  +WLG
Sbjct: 104 LLL--YVAFVLA-PALVELRNWLG 124


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: 273
Number of extensions: 12
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 377
Length of database: 273
Length adjustment: 28
Effective length of query: 349
Effective length of database: 245
Effective search space:    85505
Effective search space used:    85505
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