GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagX in Bacteroides clarus YIT 12056

Align DUF1624 domain-containing protein (characterized, see rationale)
to candidate WP_009121798.1 BUB52_RS13780 DUF1624 domain-containing protein

Query= uniprot:L0FVP4
         (369 letters)



>NCBI__GCF_900129655.1:WP_009121798.1
          Length = 396

 Score =  226 bits (575), Expect = 1e-63
 Identities = 148/397 (37%), Positives = 218/397 (54%), Gaps = 40/397 (10%)

Query: 4   QRILALDVFRGITIFAMILVNNPGSWSHVYAPLLHAKWHGCTPTDLIFPFFLFIVGVAIE 63
           +RILALD+ RG+TI  MI+VNNPG+W+H+YAPL HA+W+G TPTDL+FPFF+FI+G++  
Sbjct: 9   KRILALDILRGVTIAGMIMVNNPGTWAHIYAPLRHAEWNGLTPTDLVFPFFMFIMGISTY 68

Query: 64  LSL-----------GGQLKKGTPKGFLLRKSLIRALKL----------IGLGLLL-TAIP 101
           +SL           G ++ K T   FL+  ++    K           I  G  L  ++ 
Sbjct: 69  ISLKKYNFEFSRAVGMKILKRTILIFLIGMAIGWFSKFCYYWTSPTEGISFGAQLWESVW 128

Query: 102 YFDLAHLRFPGVLQRIGLVYFISTVMYLYWSPKALVFSSGILLIGYWLCMTFIPVPGIGP 161
            FD   +R  GV+QR+ L Y  + ++ L    + + +    LL GY++ +    V G G 
Sbjct: 129 TFD--RIRILGVMQRLALCYGATAIIALTVKHRNIPYLIATLLTGYFILL----VCGNGF 182

Query: 162 ANLEPGTNLAAWIDQQVLT-GHMWSQTKTWDPEGLFSTLPAIVTCLLGVACGKILTGN-- 218
           A  +  TN+ + ID+ +LT  HM+      DPEGL ST+P+I   LLG   G+++  N  
Sbjct: 183 AYND--TNILSVIDRTILTPAHMYKDNGI-DPEGLLSTIPSIAHVLLGFCVGRMMLENGK 239

Query: 219 ------SSHKARLTKWGIAGVTLVFGGLAWSLFFPLNKALWTSSFVLYTAGWAFLGLAAC 272
                 S   + L K  +AG  L F G   S   P+NK +W+ +FVL T G A   LA  
Sbjct: 240 ANEDRESMLNSHLIKLFLAGTILTFSGFLLSYGCPINKKIWSPTFVLTTCGLASSFLALL 299

Query: 273 YWILDVKGWKKWSLPFVIYGMNAITVFFLSGVIAKLFGLIKVNWEGTRVSLKLFLQEALF 332
            WI+DVKG+KKWSL F  +G+N + ++ L GV++ LFG I   W  + +S+  FL + L 
Sbjct: 300 IWIIDVKGYKKWSLFFESFGVNPLFMYVLGGVLSILFGSISFPWGASSISIHGFLYKILL 359

Query: 333 NGWLAPKDASLCGAILMMIILFIPAYFMWKRNIIIKV 369
                    SL  A+L + I +   Y ++KR I IK+
Sbjct: 360 MPVFGETGGSLAYALLFVGINWCIGYQLYKRKIYIKL 396


Lambda     K      H
   0.329    0.145    0.486 

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: 547
Number of extensions: 38
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: 369
Length of database: 396
Length adjustment: 30
Effective length of query: 339
Effective length of database: 366
Effective search space:   124074
Effective search space used:   124074
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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