GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Methanospirillum stamsii Pt1

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_109939172.1 DLD82_RS00420 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= TCDB::Q52666
         (263 letters)



>NCBI__GCF_003173335.1:WP_109939172.1
          Length = 376

 Score =  135 bits (340), Expect = 1e-36
 Identities = 81/234 (34%), Positives = 130/234 (55%), Gaps = 10/234 (4%)

Query: 33  GQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVDGIELTSDLKN 92
           G    L++I+ +V +GE  V+ G SG GKST++RC+NRL    +G I++DG ++ S    
Sbjct: 19  GHVVALKNISFSVKKGEIFVLMGLSGCGKSTLLRCLNRLISPTAGSILLDGEDIASVSTE 78

Query: 93  IDKV--RSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYYLEKVKIPEQ 150
             +   RS +GMVFQ F L PH  I +N+    + ++ +   E    A   L+ V +   
Sbjct: 79  RMRTIRRSRMGMVFQSFALLPHKNIQDNVAFG-LEIQGISAEERAGIAKETLDLVGLSGY 137

Query: 151 AQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDP----EMIKEVLDTMIQLAEE 206
              YP QLSGG +QRV +AR++   P I+L DE  SALDP    +M  E+LD   +L + 
Sbjct: 138 ENSYPDQLSGGMKQRVGLARAIASSPDILLMDEAFSALDPMIRRDMQNELLDIQDRLEK- 196

Query: 207 GMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLSQI 260
             T++ V+H++  A  +  R+  M  G+IV+   P +    P++E  ++F+  +
Sbjct: 197 --TIIFVSHDLDEALKLGTRIGLMKAGEIVQIGTPEEILTQPKNEFVERFVEDV 248


Lambda     K      H
   0.320    0.134    0.391 

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: 178
Number of extensions: 9
Number of successful extensions: 4
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: 263
Length of database: 376
Length adjustment: 27
Effective length of query: 236
Effective length of database: 349
Effective search space:    82364
Effective search space used:    82364
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: 48 (23.1 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