GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0028 in Paraburkholderia bryophila 376MFSha3.1

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate H281DRAFT_01031 H281DRAFT_01031 peptide/nickel transport system ATP-binding protein

Query= TCDB::Q9WXN5
         (330 letters)



>FitnessBrowser__Burk376:H281DRAFT_01031
          Length = 377

 Score =  181 bits (458), Expect = 3e-50
 Identities = 107/311 (34%), Positives = 166/311 (53%), Gaps = 18/311 (5%)

Query: 21  SVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIF--MNMVKPLTLVDGKIFLRVNGEF 78
           +V AV+ +SF +   E   +VGESGCGK+TL  ++   ++  +   L  G+      G  
Sbjct: 39  TVHAVNEVSFAVHTGETFAIVGESGCGKSTLGRMLLRLIDATQGRVLYQGEDITHWQG-- 96

Query: 79  VELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEE--ELLDK 136
            +L  + RD          + II Q    +L P + + + +      HG+     E  ++
Sbjct: 97  AKLRRLRRD----------MQIIFQDPFASLNPGMTVGQIIGEPVAFHGLASSGSECRER 146

Query: 137 ARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVL 196
             +   +VGL P + +RYP E SGG RQR  IA A    P L++ DEP SALDV  Q  +
Sbjct: 147 VAQLLTKVGLQPAYAQRYPHEFSGGQRQRIGIARALAGEPKLIVGDEPVSALDVSVQAQV 206

Query: 197 LKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQ 256
           + +L  +K + +  ++I + HD+A +R ++DR+ +MY G+IVE A V+ L + PLHPYTQ
Sbjct: 207 INLLESLKAE-LGLTLIMVAHDLAVIRHMSDRVAVMYLGEIVELAQVDELFDAPLHPYTQ 265

Query: 257 GLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIEP 316
            L  ++    P  ++R    + G  P+   PP GCRFH RCPHA   C ++ P    +  
Sbjct: 266 ALLRAIPASSPH-ERRTKPALQGDLPSPTAPPPGCRFHTRCPHAKPRCVQERPLSETLPG 324

Query: 317 GRRVACWLYME 327
           GR+VAC  + +
Sbjct: 325 GRQVACHFWRD 335


Lambda     K      H
   0.321    0.138    0.405 

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: 309
Number of extensions: 17
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: 330
Length of database: 377
Length adjustment: 29
Effective length of query: 301
Effective length of database: 348
Effective search space:   104748
Effective search space used:   104748
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