GapMind for catabolism of small carbon sources

 

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

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Btheta:350819
          Length = 463

 Score =  192 bits (488), Expect = 1e-53
 Identities = 104/254 (40%), Positives = 154/254 (60%), Gaps = 7/254 (2%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I V +VSK F  G   ALD+V +N++ GE   ILGPSG GKTT +R+IAG    S GE+ 
Sbjct: 10  IEVSHVSKFF--GDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIR 67

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEE 123
              + +        PP  R +  VFQ +AL+P+L  ++NIAF L   K  K+ I K+V+ 
Sbjct: 68  ISGKEITQT-----PPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKA 122

Query: 124 VAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALV 183
             K++ +          LSGGQQQRVA+ARA+V +P +LLLDEP + LD +MR   +  +
Sbjct: 123 ALKMVGMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMEL 182

Query: 184 KEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGE 243
           KE+   LG+T + V+HD  +   ++D + V+ +GK+ Q+G P D+Y+ P++  VA  IGE
Sbjct: 183 KEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGE 242

Query: 244 INELEGKVTNEGVV 257
            N L G + ++ +V
Sbjct: 243 SNILNGTMIHDKLV 256



 Score = 31.6 bits (70), Expect = 4e-05
 Identities = 32/133 (24%), Positives = 58/133 (43%), Gaps = 4/133 (3%)

Query: 221 QVGKPEDLYDNPVSIQVASLIGEINELEGKVTNEGVV--IGSLRFPVSVSSDRAIIGIRP 278
           +VG    L   P  I +       N  EGK+ +   V  +G      SV    +   ++ 
Sbjct: 330 EVGAEVGLLVKPFDIHIMKKERVCNTFEGKLQDATHVEFLGCTFECASVEGLESGTDVKV 389

Query: 279 EDVKLSKDVIKDDSWILVGKGKVKVIGYQGGLFRITITPLDSEEEIFTYSDHPIHSGEEV 338
           E V   K +++D+       G+VK I Y+G  + +T+   D +E +F  ++     G+ V
Sbjct: 390 E-VDFDKVILQDNEEDGTLTGEVKFILYKGDHYHLTVWS-DWDENVFVDTNDVWDDGDRV 447

Query: 339 LVYVRKDKIKVFE 351
            + +  D I+V +
Sbjct: 448 GITIPPDAIRVIK 460


Lambda     K      H
   0.319    0.139    0.390 

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: 390
Number of extensions: 20
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: 353
Length of database: 463
Length adjustment: 31
Effective length of query: 322
Effective length of database: 432
Effective search space:   139104
Effective search space used:   139104
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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