GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Phaeacidiphilus oryzae TH49

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q72L52
         (376 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  347 bits (890), Expect = e-100
 Identities = 194/356 (54%), Positives = 240/356 (67%), Gaps = 8/356 (2%)

Query: 14  GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIGDRLVNDVPPK 73
           G   AV   +LE  DGEF+V VGPSGCGK+T+LRM+AGLE+++ G I IG+R V  +PPK
Sbjct: 16  GDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPK 75

Query: 74  DRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKIEHLLNRKPRE 133
           DRDIAMVFQNYALYPHM V +NM F L++    K EI  +V+EAA+IL +   L+RKP+ 
Sbjct: 76  DRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAAKILDLTEFLDRKPKA 135

Query: 134 LSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRLGVTTIYVTHD 193
           LSGGQRQRVAMGRAIVREP+VFLMDEPLSNLDAKLRV  R +IA LQRRLG+TT+YVTHD
Sbjct: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITTVYVTHD 195

Query: 194 QVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVRAGVEVQGEKV 253
           QVEAMT+G R+ V+KDG +QQVDTP N+YD PAN FVAGFIGSP+MN V   +   G K 
Sbjct: 196 QVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLVEVPITDGGVK- 254

Query: 254 YLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEEENVLRGEVEVVEP 313
                  ++  +AV G A      K V +GVRPEHL + G T    E+  L   V VVE 
Sbjct: 255 -FGESVVQVSRDAV-GEAANA-GDKTVTVGVRPEHLDIVGGTEGGGEDKGLAVTVNVVEE 311

Query: 314 LGAETEIH----VAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLHAFDLETDRTI 365
           LGA+  ++    V      LV +V G      GD++ ++      H F   T + +
Sbjct: 312 LGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGETHVFSTSTGKRL 367


Lambda     K      H
   0.320    0.139    0.400 

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: 435
Number of extensions: 24
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: 376
Length of database: 369
Length adjustment: 30
Effective length of query: 346
Effective length of database: 339
Effective search space:   117294
Effective search space used:   117294
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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