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

GapMind for catabolism of small carbon sources

Aligments 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources