GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB' in Pseudomonas simiae WCS417

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate GFF967 PS417_04905 amino acid ABC transporter permease

Query= uniprot:Q31RP0
         (377 letters)



>FitnessBrowser__WCS417:GFF967
          Length = 393

 Score =  258 bits (658), Expect = 3e-73
 Identities = 151/375 (40%), Positives = 219/375 (58%), Gaps = 19/375 (5%)

Query: 14  DERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYR 73
           D +L  W++Q++ ++ V     +L +N   NL  RG++  FD+L++SAGF I +  I Y 
Sbjct: 16  DPKLRAWLFQIITIVAVVSLGWYLFNNTQTNLQHRGITSGFDFLERSAGFGIAQHLIDYT 75

Query: 74  TADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTP 133
            +DSYAR  V+GL+N+L V  IG+IL T++G + GVA  S NW++ +L+  YV V RN P
Sbjct: 76  ESDSYARVFVIGLLNTLLVTFIGVILATLLGFVIGVARLSPNWMINKLATVYVEVFRNIP 135

Query: 134 LLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLP--------WPQTPGWLVVILA 185
            LLQ++ WYF + L++P  +   ++  + ++S +G+ +P        WP      +V+  
Sbjct: 136 PLLQILFWYFAVFLTMPGPRNSHNFGDTFFVSSRGLNMPAAIAADGFWPFVVS--IVVAI 193

Query: 186 IALVLFVSWLAQRQRS---PRDWRW----LYGAIAVVTVLMLLTQLSWPQ-QLQPGQIRG 237
           +A+VL   W  +R  +   P    W    L+  I  +  L+    L W   +LQ     G
Sbjct: 194 VAIVLMARWANKRFEATGVPFHKFWAGLALFIVIPALCALIFGAPLHWEMPKLQGFNFVG 253

Query: 238 GLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQ 297
           G  L  E  AL L L  YT AFI EI+R GI SV  GQ EAA +LGL    TL ++++PQ
Sbjct: 254 GWVLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRPGPTLRKVIIPQ 313

Query: 298 ALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLTYLAI 356
           ALRVI+P L SQY+  AKNSSLA  +GYP++ +  A T LNQTG+ +EV  I M  YLAI
Sbjct: 314 ALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAI 373

Query: 357 NAVISAGMNGLQQRL 371
           +  IS  MN   +R+
Sbjct: 374 SISISLLMNWYNKRI 388


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: 380
Number of extensions: 9
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: 393
Length adjustment: 30
Effective length of query: 347
Effective length of database: 363
Effective search space:   125961
Effective search space used:   125961
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 (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