GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate H281DRAFT_00167 H281DRAFT_00167 carbohydrate ABC transporter membrane protein 1, CUT1 family

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895
         (302 letters)



>FitnessBrowser__Burk376:H281DRAFT_00167
          Length = 312

 Score =  374 bits (960), Expect = e-108
 Identities = 177/294 (60%), Positives = 229/294 (77%), Gaps = 1/294 (0%)

Query: 9   KASPFDAL-QRWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWVGLQQYMR 67
           + SP  AL  RW+PKLVLAPS++I LV  YG+I  T  LS +NS  MP Y++VGL +Y  
Sbjct: 17  RVSPMAALADRWIPKLVLAPSVVISLVFVYGFIAITGYLSLSNSRLMPRYEFVGLDRYRE 76

Query: 68  LMDNDRWWVASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIV 127
           L DND +W ++ NL  FG  FI I + LG+FLA+LLDQ+IR EG +R V+LYPMALS IV
Sbjct: 77  LFDNDVFWTSAANLGWFGIPFIGICIGLGLFLAILLDQQIRNEGALRAVFLYPMALSFIV 136

Query: 128 TGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMFLA 187
           TGTAW+W++ P +GL+K+  DWGW  F   WL D D+ ++C+VIAAVWQ++GFVMA+FLA
Sbjct: 137 TGTAWQWIMTPSIGLEKVFHDWGWTSFSFSWLGDPDKAIFCVVIAAVWQSTGFVMALFLA 196

Query: 188 GLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAG 247
           GLRGVD  I +AAQ+DGA+LPTIY KIV+PS+RPVFFS  +IL HI IK+FDLV A+TAG
Sbjct: 197 GLRGVDGEIFKAAQMDGANLPTIYRKIVIPSMRPVFFSVLLILCHITIKTFDLVVALTAG 256

Query: 248 GPGYSSDLPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELRGKRH 301
           GPG SS LPA+FMY+F+F+RGQ+G+G+AS+M+ML  V+ +LVP +Y E R  R+
Sbjct: 257 GPGTSSSLPAIFMYTFSFNRGQLGVGAASSMMMLATVVAVLVPLMYLESRSTRN 310


Lambda     K      H
   0.329    0.141    0.448 

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: 395
Number of extensions: 13
Number of successful extensions: 1
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: 302
Length of database: 312
Length adjustment: 27
Effective length of query: 275
Effective length of database: 285
Effective search space:    78375
Effective search space used:    78375
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