GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB' in Rhizorhabdus wittichii RW1

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit

Query= uniprot:Q31RP0
         (377 letters)



>NCBI__GCF_000016765.1:WP_012048835.1
          Length = 374

 Score =  226 bits (576), Expect = 8e-64
 Identities = 139/372 (37%), Positives = 207/372 (55%), Gaps = 12/372 (3%)

Query: 13  RDERLWRWVWQLLVLLVVGLGAIWLVDNLVY-NLSQRGLSLSFDWLDQSAGFNIGESAIA 71
           R  R W W    + LL+   G + +V   V  N+ ++ + LS  +L  +A F I ES +A
Sbjct: 5   RAARGWGWWLPQVALLLALAGLVLVVARTVSDNMERQDMVLSLGFLRSTAEFPIAESFLA 64

Query: 72  YRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRN 131
           Y   D+ A A VVGL NS+ +  + ++L+T+ G    +A  S + L R L+ G+V +VRN
Sbjct: 65  YAPGDTIAWAFVVGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRN 124

Query: 132 TPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIY-----LPWPQTPGWLVVILAI 186
            PL++QL+ WY  IL++ P A+     L  L+L+ +GI      +     P  + V+  +
Sbjct: 125 VPLVVQLLFWYGVILMAFPPARAAAQPLPGLFLTNRGITVTTVGITGTALPMIVTVLGGL 184

Query: 187 ALVLFVSWLAQRQRSPRDWRWLYGAIAVVTVLMLLTQLSWPQQL---QPGQIRGGLRLSL 243
            L L  +W     ++        G I   + L ++  L   + +         GGL L+ 
Sbjct: 185 TLTLITAWRGHLHKASL---CTLGTIVAGSALWIVLDLGLARDVPHFDRFNFTGGLTLTP 241

Query: 244 EFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIV 303
           EF A+L G V Y  AF  EI+RGG+  VP GQWEA+ ALGL++ Q+L  ++VPQALR+IV
Sbjct: 242 EFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQSLRLVIVPQALRMIV 301

Query: 304 PSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAG 363
           P +NSQ++   KNS+LA+ VGYPDL   A T +N TG+ +E   ILML +  + + IS  
Sbjct: 302 PPMNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGVAILMLVFFTLASAISLA 361

Query: 364 MNGLQQRLQRWG 375
           MN L  R+QR G
Sbjct: 362 MNRLNARVQRGG 373


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: 363
Number of extensions: 20
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 377
Length of database: 374
Length adjustment: 30
Effective length of query: 347
Effective length of database: 344
Effective search space:   119368
Effective search space used:   119368
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 Apr 09 2024. 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