GapMind for catabolism of small carbon sources

 

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

Align GlcU, component of Glucose, mannose, galactose porter (characterized)
to candidate H281DRAFT_01452 H281DRAFT_01452 carbohydrate ABC transporter membrane protein 2, CUT1 family

Query= TCDB::Q97UY9
         (287 letters)



>FitnessBrowser__Burk376:H281DRAFT_01452
          Length = 305

 Score =  134 bits (338), Expect = 2e-36
 Identities = 87/282 (30%), Positives = 146/282 (51%), Gaps = 19/282 (6%)

Query: 15  YLALAIVSVIWLIPVYAMLINGFKSNFEVLSTPVLVPPTKITFEAYVSVLLSLAKPLI-- 72
           YL L   ++ +L+P+Y ML+  FK   E+    +L  P   T  A+ +   S    L   
Sbjct: 33  YLFLLSAALFFLLPLYVMLVTSFKPMSEIRLGNLLALPAHFTLHAWSAAWESACTGLDCN 92

Query: 73  -------NSLIIVIPTSFISAFLGAMGAYFFYTLSYSFSRASSAISDVLFSLISLATFIP 125
                  NS+ IV+P++  S  +GA+  Y     + SF R   A   VLF ++ +  FIP
Sbjct: 93  GIQVGFWNSVRIVVPSTVFSIAIGAVNGY-----ALSFWRPRGA--GVLFGVLLMGAFIP 145

Query: 126 QEATLLPLTRLIVSMGLLDSYIGIIFALLIFYIPTGALLMSMFISVIPRSLIEAAKMDGT 185
            +  + PL R++ S+ L  S  GI+    IF +P   LL   + + IP+ L +AA++DG 
Sbjct: 146 VQVMVYPLVRVLASVHLFSSLPGIVVIHTIFGMPVMTLLFRNYYASIPQELFKAARIDGG 205

Query: 186 GDLKIFMKIVFPLSMPGFISTLIFIIIQAWNNFFIPLVLVTTPGMKLT-SIAVLSYSGAY 244
           G  +IF++++ P+S P  +  +I  +   WN+F + LV   T  + +T  +  +  +   
Sbjct: 206 GFWRIFVQLMLPMSTPIIVVAVIMQVTGIWNDFILGLVFAGTKNLPMTVQLNNIINTTTG 265

Query: 245 GTLYNDTFAAGMVASIIPLAIFVFLGRYFIRGLMALGGGGKG 286
             LYN   AA ++ S++PLA++   GR+F+RG+ +  G  KG
Sbjct: 266 ERLYNVNMAATILTSLVPLAVYFISGRWFVRGIAS--GAVKG 305


Lambda     K      H
   0.330    0.144    0.417 

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: 254
Number of extensions: 13
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: 287
Length of database: 305
Length adjustment: 26
Effective length of query: 261
Effective length of database: 279
Effective search space:    72819
Effective search space used:    72819
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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