GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztA in Photobacterium gaetbulicola Gung47

Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_082060698.1 H744_RS20715 transporter substrate-binding domain-containing protein

Query= TCDB::Q52663
         (338 letters)



>NCBI__GCF_000940995.1:WP_082060698.1
          Length = 377

 Score =  356 bits (914), Expect = e-103
 Identities = 170/319 (53%), Positives = 228/319 (71%), Gaps = 1/319 (0%)

Query: 20  ASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCKAVAAAVLGDPMKVKYV 79
           AS+ TL  V+ +G L CG   GL GF+ P+  G ++G DV  C+AVAAA+LGD  KVKY+
Sbjct: 60  ASSETLAKVQKQGYLQCGVTTGLPGFSNPNEKGEWEGLDVEFCQAVAAAILGDKTKVKYI 119

Query: 80  PLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYYDGQGFMVNKSLGVSSAK 139
           PLT + RFTAL SGE+D+L RN+TWT  RDT L ++F  VNYYDGQGFM+NK+L + SA 
Sbjct: 120 PLTAKERFTALQSGEIDLLSRNTTWTLHRDTALGINFAGVNYYDGQGFMINKALEIESAA 179

Query: 140 ELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQKFAAGACDSYTTDASGL 199
           ELDGA +CVQ+GTTTE+NLAD+F+   M YTPV     A+  + F AG CD+ TTD SGL
Sbjct: 180 ELDGAAVCVQSGTTTELNLADYFRHREMKYTPVVFDTAAQTVKGFEAGRCDALTTDQSGL 239

Query: 200 ASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRWSFYALVAAEEYGITKANL 259
            + R  LP+ +  V+LP+IISKEPLGP VR GD+ W +IV+W+  A++ AEE G++  N+
Sbjct: 240 YALRLNLPDPSSAVVLPDIISKEPLGPAVRQGDDQWFNIVKWTLNAMITAEELGVSSHNV 299

Query: 260 EEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGNYGEVFEANIGASTSIGLA 319
           +++  S  +P IRRL+G +G  GK +GL++D+A + I   GNYGE FE  +G S+ + + 
Sbjct: 300 DDMKMS-NDPNIRRLIGADGPKGKGLGLNDDWAYQVIKQVGNYGESFERTVGMSSPLEIK 358

Query: 320 RGLNAQWTQGGLMYAPPFR 338
           RG+NA W  GGL+YAPP R
Sbjct: 359 RGINALWNDGGLLYAPPMR 377


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: 347
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: 338
Length of database: 377
Length adjustment: 29
Effective length of query: 309
Effective length of database: 348
Effective search space:   107532
Effective search space used:   107532
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 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