GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Bacteroides thetaiotaomicron VPI-5482

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate 350090 BT0562 putative ABC transporter ATP-binding protein (NCBI ptt file)

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__Btheta:350090
          Length = 489

 Score =  110 bits (275), Expect = 5e-29
 Identities = 63/189 (33%), Positives = 113/189 (59%), Gaps = 3/189 (1%)

Query: 10  PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKI 69
           P++ V+ +   Y K V+ L+ V+F VE GE+  +IGP+GAGKSTL + +  LL    G  
Sbjct: 6   PIVVVKEISKSYGK-VEALKEVSFAVEQGEVFGLIGPDGAGKSTLFRILTTLLLADKGTA 64

Query: 70  TFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAM 129
           T  G ++  +   + +R  + Y+P   +++  LSVEENLE  A + +  +Q   D I  +
Sbjct: 65  TVNGLDV--VTDYKQIRTKVGYMPGRFSLYQDLSVEENLEFFATVFHTLIQENYDLIKDI 122

Query: 130 FPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQI 189
           + ++   +++RAG LSGG +Q LA+  +L+ +P +L LDEP+  + P+   + ++ ++ +
Sbjct: 123 YQQIEPFKKRRAGALSGGMKQKLALSCSLIHKPDILFLDEPTTGVDPVSRKEFWQMLRNL 182

Query: 190 NQEGTAIIL 198
            ++G  II+
Sbjct: 183 RKQGITIIV 191



 Score = 75.1 bits (183), Expect = 2e-18
 Identities = 59/219 (26%), Positives = 105/219 (47%), Gaps = 10/219 (4%)

Query: 6   QNFTPLLEVENVHA--GYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLT 63
           Q   P++EVE +    G+   VD    ++F+V+ GE+   +G NGAGK+T  + + GL  
Sbjct: 242 QMAAPVIEVEQLTKSFGHFTAVD---HISFQVQRGEIFGFLGANGAGKTTAMRMLCGLSR 298

Query: 64  PHTGKITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLK 123
           P +G     G +I   +  + V+  + Y+ Q  +++  L V EN+ + A I       ++
Sbjct: 299 PTSGVGKVAGYDI--FREAEQVKRHIGYMSQKFSLYEDLKVWENIRLFAGIYGMKEMEIE 356

Query: 124 DKIFAMFPRL--SDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQ 181
           +K   +  RL  +D R      L  G +Q LA   ++  EP ++ LDEP+  + P    Q
Sbjct: 357 EKTDELLERLGFADERDTLVKNLPLGWKQKLAFSVSIFHEPKIVFLDEPTGGVDPATRRQ 416

Query: 182 VFEQVKQINQEGTAIILVEQNARKALEMADRGYVLESGR 220
            +E + Q    G  + +      +A E  +R  ++  G+
Sbjct: 417 FWELIYQAADRGITVFVTTHYMDEA-EYCNRISIMVDGQ 454


Lambda     K      H
   0.317    0.136    0.377 

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: 272
Number of extensions: 15
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 247
Length of database: 489
Length adjustment: 29
Effective length of query: 218
Effective length of database: 460
Effective search space:   100280
Effective search space used:   100280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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