GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztA in Methylocystis bryophila S285

Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_245299991.1 B1812_RS19680 amino acid ABC transporter substrate-binding protein

Query= TCDB::Q52663
         (338 letters)



>NCBI__GCF_002117405.1:WP_245299991.1
          Length = 350

 Score =  256 bits (655), Expect = 5e-73
 Identities = 136/340 (40%), Positives = 205/340 (60%), Gaps = 10/340 (2%)

Query: 7   FGSVALAALVAG---AASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCK 63
           FG VA A  +A    + ++STL +++ RG ++CG+     GFA  D  G + GFD+  C+
Sbjct: 13  FGLVAGAPRLAAQPESKASSTLQEIRRRGVVVCGATAPAPGFAVMDEAGSWSGFDIDFCR 72

Query: 64  AVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYYD 123
           A+A A L DP K++   L  + R  AL SG+VDVL+  + WT +R+    L + A+++Y 
Sbjct: 73  ALAVAALDDPQKIRIETLQQKQRLPALHSGDVDVLLSGAPWTEAREAGHQLLYGAISFYG 132

Query: 124 GQGFMVNKSLGVSSAKELDGA-----TICVQTGTTTEMNLADFFKANNMTYTPVNIADDA 178
           GQGF+  ++ G  + +   GA      +CVQ G ++E+NLA F++ + + Y PV      
Sbjct: 133 GQGFLGRRAWG-PTGEPWRGAGGTPPRVCVQQGGSSELNLAQFYREHGVAYRPVAFGSLE 191

Query: 179 EGQQKFAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDI 238
           E  + + AG CD ++ D   L   R+ L    D V+ P +ISK PLGP+VR GD+ W ++
Sbjct: 192 EAARAYDAGDCDLFSADLVELHQWRSRLQKPDDHVVAPALISKSPLGPIVRQGDDQWFNV 251

Query: 239 VRWSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILA 298
           VRW+ +A+V AEE G+  A   + A S+  P++RRL+G +GD G+ +GL  D+A R I  
Sbjct: 252 VRWTLFAMVDAEELGV-DAKTVDAALSSDIPDLRRLVGSDGDFGEGLGLRPDWAYRVIHE 310

Query: 299 SGNYGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338
            GNY EVF+ N+G S+   + R  NA W++GGLMYAPP R
Sbjct: 311 VGNYAEVFDRNLGKSSPFAMERRQNALWSKGGLMYAPPVR 350


Lambda     K      H
   0.316    0.132    0.384 

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: 297
Number of extensions: 12
Number of successful extensions: 3
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: 338
Length of database: 350
Length adjustment: 29
Effective length of query: 309
Effective length of database: 321
Effective search space:    99189
Effective search space used:    99189
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 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