GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Nitratifractor salsuginis DSM 16511

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease

Query= CharProtDB::CH_011913
         (426 letters)



>NCBI__GCF_000186245.1:WP_013554635.1
          Length = 384

 Score =  275 bits (704), Expect = 1e-78
 Identities = 160/409 (39%), Positives = 239/409 (58%), Gaps = 33/409 (8%)

Query: 20  DTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYS 79
           D + R I  QI+ + LF+  L ++  N   N+E +G    F+FL   AG+D+ ++ IP++
Sbjct: 7   DEKIRGILYQIIAITLFVGFLFYIAQNTAHNIEQRGIKTGFAFLHDTAGFDITESPIPFT 66

Query: 80  NDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIP 139
              TH +    GLLNTL+VS  G + ++++G +IG+ RLS NWL+ RI   Y+ETFRNIP
Sbjct: 67  PASTHLKVFEVGLLNTLIVSFWGIVFSSLIGLLIGIWRLSPNWLINRIAAAYIETFRNIP 126

Query: 140 LLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFD 199
           +LL IL    ++  T P                  + S+ FF++V + NRG  +P   F 
Sbjct: 127 VLLQILFWYNVVLATLP----------------STRHSLNFFNAVFINNRGFFMPKLVFQ 170

Query: 200 HSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLIL 259
                 D  W +  ++ A AI+ ++    W        AK  QE TG +   +   +++L
Sbjct: 171 ------DGAWMIGAAIVA-AIIGIIFVHRW--------AKKRQEETGEQFPVFLTGIILL 215

Query: 260 FA-PISA-LLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGI 317
              P+ A L+ G      YP++  F+F GG      F ALL AL++YTA FIAE +R+GI
Sbjct: 216 IGLPLLAYLIAGRPVTAVYPELHGFNFRGGKTFTPEFLALLFALSIYTATFIAEAIRSGI 275

Query: 318 QAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDL 377
           +A+ +GQ EAA +LGL P + + LVILPQA+R+ +P +I+Q+LNL KNSSLA A+ Y +L
Sbjct: 276 EAVPKGQKEAATSLGLSPLQQLRLVILPQAVRIAIPSIINQYLNLIKNSSLAAAIGYPEL 335

Query: 378 RGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426
                G +LNQTG+ LE +L+ ML YL ISL +S ++N +N  +K+KER
Sbjct: 336 VTIFAGTSLNQTGQALEILLITMLTYLLISLIVSLILNWFNAKMKIKER 384


Lambda     K      H
   0.326    0.139    0.419 

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: 361
Number of extensions: 14
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: 426
Length of database: 384
Length adjustment: 31
Effective length of query: 395
Effective length of database: 353
Effective search space:   139435
Effective search space used:   139435
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