GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB' in Nitratifractor salsuginis DSM 16511

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease

Query= uniprot:Q31RP0
         (377 letters)



>NCBI__GCF_000186245.1:WP_013554635.1
          Length = 384

 Score =  232 bits (591), Expect = 1e-65
 Identities = 131/378 (34%), Positives = 224/378 (59%), Gaps = 17/378 (4%)

Query: 11  FWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAI 70
           F RDE++   ++Q++ + +      ++  N  +N+ QRG+   F +L  +AGF+I ES I
Sbjct: 4   FLRDEKIRGILYQIIAITLFVGFLFYIAQNTAHNIEQRGIKTGFAFLHDTAGFDITESPI 63

Query: 71  AYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVR 130
            +  A ++ +   VGL+N+L V   G++ +++IG L G+   S NWL+ +++  Y+   R
Sbjct: 64  PFTPASTHLKVFEVGLLNTLIVSFWGIVFSSLIGLLIGIWRLSPNWLINRIAAAYIETFR 123

Query: 131 NTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWP--QTPGWLV---VILA 185
           N P+LLQ++ WY  +L +LP+ +   ++  +++++ +G ++P    Q   W++   ++ A
Sbjct: 124 NIPVLLQILFWYNVVLATLPSTRHSLNFFNAVFINNRGFFMPKLVFQDGAWMIGAAIVAA 183

Query: 186 IALVLFV-SWLAQRQRSPRDW--RWLYGAIAVVTVLMLLTQLS-------WPQQLQPGQI 235
           I  ++FV  W  +RQ    +    +L G I ++ + +L   ++       +P +L     
Sbjct: 184 IIGIIFVHRWAKKRQEETGEQFPVFLTGIILLIGLPLLAYLIAGRPVTAVYP-ELHGFNF 242

Query: 236 RGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVV 295
           RGG   + EF ALL  L  YT  FI E IR GI +VP GQ EAA +LGL+  Q L  +++
Sbjct: 243 RGGKTFTPEFLALLFALSIYTATFIAEAIRSGIEAVPKGQKEAATSLGLSPLQQLRLVIL 302

Query: 296 PQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLTYL 354
           PQA+R+ +PS+ +QY+   KNSSLA A+GYP+L    A T+LNQTG+ +E+ LI MLTYL
Sbjct: 303 PQAVRIAIPSIINQYLNLIKNSSLAAAIGYPELVTIFAGTSLNQTGQALEILLITMLTYL 362

Query: 355 AINAVISAGMNGLQQRLQ 372
            I+ ++S  +N    +++
Sbjct: 363 LISLIVSLILNWFNAKMK 380


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: 362
Number of extensions: 16
Number of successful extensions: 4
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: 384
Length adjustment: 30
Effective length of query: 347
Effective length of database: 354
Effective search space:   122838
Effective search space used:   122838
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.

Links

Downloads

Related tools

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