GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Streptococcus oralis 7747

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_000742904.1 HK29_RS03610 ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_000382825.1:WP_000742904.1
          Length = 385

 Score =  203 bits (517), Expect = 5e-57
 Identities = 111/283 (39%), Positives = 175/283 (61%), Gaps = 10/283 (3%)

Query: 7   KNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDD 66
           KNVSKVF+      L ++N  +E G+ + +LG SG+GK+T + IIAGL   +TG++  D 
Sbjct: 9   KNVSKVFEDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTGDILLDG 68

Query: 67  RLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAK 126
             +       +P   R +  VFQ++AL+P++  FEN+AFPL   K+ K+EI +RV EV K
Sbjct: 69  VRIND-----IPTNKRDVHTVFQSYALFPHMNVFENVAFPLRLRKVDKKEIEQRVAEVLK 123

Query: 127 ILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEV 186
           ++ +        R+LSGGQ+QRVA+ARA++  P ++LLDEP S LD ++R   +  ++E+
Sbjct: 124 MVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYELREL 183

Query: 187 QSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINE 246
           Q RLG+T + V+HD  +  A++D + V+  G++VQ G P D+YD P++  VA+ IGE N 
Sbjct: 184 QQRLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIGESNI 243

Query: 247 LEGKVTNEGVV-IGSLRFPV----SVSSDRAIIGIRPEDVKLS 284
           L G +  + +V     RF         ++   I IRPED++++
Sbjct: 244 LPGTMIEDYLVEFNGKRFEAVDGGMKPNEPVEIVIRPEDLRIT 286


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: 383
Number of extensions: 10
Number of successful extensions: 2
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: 353
Length of database: 385
Length adjustment: 30
Effective length of query: 323
Effective length of database: 355
Effective search space:   114665
Effective search space used:   114665
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: 49 (23.5 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