GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Paraburkholderia bryophila 376MFSha3.1

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate H281DRAFT_01031 H281DRAFT_01031 peptide/nickel transport system ATP-binding protein

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__Burk376:H281DRAFT_01031
          Length = 377

 Score =  182 bits (462), Expect = 1e-50
 Identities = 104/303 (34%), Positives = 171/303 (56%), Gaps = 15/303 (4%)

Query: 26  YALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFK 85
           +A+ +VS +++ G+   ++GESG GK+TLGR+++ L   T G V+Y G +I   +    +
Sbjct: 41  HAVNEVSFAVHTGETFAIVGESGCGKSTLGRMLLRLIDATQGRVLYQGEDITHWQGAKLR 100

Query: 86  KYRKDVQLIPQDPYSTLPFNKTVEEILVAPI-LRWEKINKDELRKRLINLLELVKLTPAE 144
           + R+D+Q+I QDP+++L    TV +I+  P+       +  E R+R+  LL  V L PA 
Sbjct: 101 RLRRDMQIIFQDPFASLNPGMTVGQIIGEPVAFHGLASSGSECRERVAQLLTKVGLQPA- 159

Query: 145 EFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLN 204
            +  +YPH+ SGGQ+QR+ IAR+L+  P++IV DEPV+ +D S++  ++N L  +K  L 
Sbjct: 160 -YAQRYPHEFSGGQRQRIGIARALAGEPKLIVGDEPVSALDVSVQAQVINLLESLKAELG 218

Query: 205 LTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKLTPS 264
           LT++ + HD+ + R   H+ D+    VM+ G IVE A ++E+   PLHPYT  L++  P+
Sbjct: 219 LTLIMVAHDLAVIR---HMSDR--VAVMYLGEIVELAQVDELFDAPLHPYTQALLRAIPA 273

Query: 265 IDNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDICKNEEP--KLFKYSHEVACFLY 317
                +     +  +         GC +  RCP A   C  E P  +      +VAC  +
Sbjct: 274 SSPHERRTKPALQGDLPSPTAPPPGCRFHTRCPHAKPRCVQERPLSETLPGGRQVACHFW 333

Query: 318 GKV 320
             V
Sbjct: 334 RDV 336


Lambda     K      H
   0.321    0.141    0.410 

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: 308
Number of extensions: 15
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: 324
Length of database: 377
Length adjustment: 29
Effective length of query: 295
Effective length of database: 348
Effective search space:   102660
Effective search space used:   102660
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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