GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bgtB' in Pseudomonas stutzeri RCH2

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate GFF3103 Psest_3162 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= uniprot:Q31RP0
         (377 letters)



>lcl|FitnessBrowser__psRCH2:GFF3103 Psest_3162 amine acid ABC
           transporter, permease protein, 3-TM region,
           His/Glu/Gln/Arg/opine family
          Length = 394

 Score =  242 bits (617), Expect = 1e-68
 Identities = 149/379 (39%), Positives = 215/379 (56%), Gaps = 16/379 (4%)

Query: 8   QGPFWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGE 67
           + PF  D R+  WV+Q+L +L V     +L  N   NL+ RG++  F +L+ +AGF I +
Sbjct: 12  RSPF-TDPRIRAWVFQVLAVLAVVAFGWYLFHNTQTNLAHRGITSGFGFLNNAAGFGISQ 70

Query: 68  SAIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVA 127
             I Y  +D+Y R   VGL+N+L V  IG+ L TV+G + GV   S NWL+RQL+  Y+ 
Sbjct: 71  HLIDYSESDTYGRVFWVGLLNTLLVSVIGIFLATVMGFILGVGRLSSNWLIRQLATLYIE 130

Query: 128 VVRNTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQTPG-----WLVV 182
           + RN P LL +   YF ++  LP  +        ++++ +G+ +P P         WL +
Sbjct: 131 IFRNIPPLLLIFFVYFAVISPLPGPRNSLSLWDVVFVNNRGVQMPAPSAGDGFWAFWLAL 190

Query: 183 ILA-IALVLFVSWLAQRQRS-----PRDWR--WLYGAIAVVTVLMLLTQLSWP-QQLQPG 233
           ++A +A+V+   W   R+ +     P  W    L+ AI  +   +     +W   +LQ  
Sbjct: 191 LVALVAVVVLNRWARARRHATGRMFPVFWTSPGLFLAIPWLMTFIAGAPFTWEVPELQRF 250

Query: 234 QIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQI 293
            IRGG  +  E  ++++ L  YT AFI E +R GI SV  GQ EAAA+LGL   Q L  +
Sbjct: 251 NIRGGWVVIPELVSIVVALSVYTAAFIGETVRSGIQSVSHGQTEAAASLGLRPGQVLRLV 310

Query: 294 VVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLT 352
           +VPQALRVIVP L SQY+  AKNSSLA A+GYPD+ +  A T LNQTG+ +E   I M  
Sbjct: 311 IVPQALRVIVPPLTSQYLNLAKNSSLAAAIGYPDMVSLFAGTVLNQTGQAIETMAITMSV 370

Query: 353 YLAINAVISAGMNGLQQRL 371
           YLAI+  IS  MN   +R+
Sbjct: 371 YLAISISISLLMNWYNKRI 389


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: 438
Number of extensions: 25
Number of successful extensions: 3
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: 394
Length adjustment: 30
Effective length of query: 347
Effective length of database: 364
Effective search space:   126308
Effective search space used:   126308
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, 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