GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natE 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)



>lcl|FitnessBrowser__Btheta:350090 BT0562 putative ABC transporter
           ATP-binding protein (NCBI ptt file)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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