GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Methylocystis bryophila S285

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_085770045.1 B1812_RS01630 ABC transporter ATP-binding protein

Query= SwissProt::P17328
         (400 letters)



>NCBI__GCF_002117405.1:WP_085770045.1
          Length = 352

 Score =  168 bits (426), Expect = 2e-46
 Identities = 98/285 (34%), Positives = 160/285 (56%), Gaps = 11/285 (3%)

Query: 29  LSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLID 88
           L+ E+  ++ G ++ + D S+ +  GE F ++G SG GK+T++RL+     P  G++ ++
Sbjct: 7   LAIERASKRFGSTVALDDVSVDVAPGEFFALLGPSGCGKTTLMRLIAGFERPDSGRLTLE 66

Query: 89  GVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDA 148
           G D+A +         ++ I M+FQS+AL PH+ V +N AFG+   G+A  + +++  + 
Sbjct: 67  GRDLAGLPP------HQRPINMMFQSYALFPHLDVFENIAFGLRRKGLAQDDVKKRVQEL 120

Query: 149 LRQVGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELV 208
           L  V L  +      +LSGG +QRV LARALA  P +LL+DE   ALD  +R E Q +L 
Sbjct: 121 LDVVQLGGFNARRIHQLSGGQKQRVALARALAPGPKLLLLDEPLGALDRKLREETQLQLK 180

Query: 209 KLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGV 268
           ++Q K     V ++HD DEA+ + DRIA+M+ G++ Q+G P ++   P N +V  F    
Sbjct: 181 QIQRKLNTAFVIVTHDQDEALALADRIAVMRAGKIEQIGAPPDVYRRPQNRFVADFIGAT 240

Query: 269 DI--SQVFSAKDIARRSPVGLIRK---TPGFGPRSALKLLQDEDR 308
           ++    V  A  +   +P G I +   T   G R+AL L   + R
Sbjct: 241 NLIEGHVSRADGVWFVAPFGKIARAVCTLDDGARAALSLRPQDIR 285


Lambda     K      H
   0.319    0.137    0.378 

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: 301
Number of extensions: 13
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: 400
Length of database: 352
Length adjustment: 30
Effective length of query: 370
Effective length of database: 322
Effective search space:   119140
Effective search space used:   119140
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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