GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SMc04257 in Phaeobacter inhibens BS107

Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate GFF3854 PGA1_78p00180 putative sn-glycerol-3-phosphate transport system permease protein UgpE

Query= reanno::Smeli:SMc04257
         (305 letters)



>lcl|FitnessBrowser__Phaeo:GFF3854 PGA1_78p00180 putative
           sn-glycerol-3-phosphate transport system permease
           protein UgpE
          Length = 309

 Score =  503 bits (1296), Expect = e-147
 Identities = 236/303 (77%), Positives = 279/303 (92%), Gaps = 3/303 (0%)

Query: 6   ETAPGGPMA---GPRGRKPRRTLSRRNIIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIR 62
           +T  G P+    GPRG KP+  +SRRN+++YGTL+++ALYYLLPLYVM+VTSLKGMPEIR
Sbjct: 7   QTPKGSPVRILDGPRGAKPKTRVSRRNVMLYGTLLLIALYYLLPLYVMVVTSLKGMPEIR 66

Query: 63  VGNIFAPPLEITFEPWVKAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYA 122
           +GNIF+PP+EITF+PW+KAW+EACTG+NCDGLSRGF NS++I VPSV +SIAIASVNGYA
Sbjct: 67  LGNIFSPPVEITFQPWIKAWSEACTGINCDGLSRGFGNSIKILVPSVALSIAIASVNGYA 126

Query: 123 LANWRFKGADLFFTILIVGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILT 182
           LANWRFKG++ FFTILI+GAFIPYQ M+YPIVI+LRE+ + G+L GL++VH+IFGMPILT
Sbjct: 127 LANWRFKGSETFFTILIIGAFIPYQTMLYPIVIILRELKLMGSLWGLVLVHSIFGMPILT 186

Query: 183 LLFRNYFAGLPEELFKAARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGV 242
           LLFRNYF+ LPEELFKAARVDGAGFW IY ++M+PMS+PIFVVAMILQVTGIWNDFLFGV
Sbjct: 187 LLFRNYFSSLPEELFKAARVDGAGFWGIYLRVMVPMSIPIFVVAMILQVTGIWNDFLFGV 246

Query: 243 VFTRPEYYPMTVQLNNIVNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGA 302
           ++T+PE YPMTVQLNNIVNSVQGVKEYNVNMAAT+LTGLVPL +Y VSG+LFVRGIAAGA
Sbjct: 247 IYTKPETYPMTVQLNNIVNSVQGVKEYNVNMAATLLTGLVPLVIYLVSGKLFVRGIAAGA 306

Query: 303 VKG 305
           VKG
Sbjct: 307 VKG 309


Lambda     K      H
   0.329    0.145    0.450 

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: 411
Number of extensions: 10
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: 305
Length of database: 309
Length adjustment: 27
Effective length of query: 278
Effective length of database: 282
Effective search space:    78396
Effective search space used:    78396
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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