GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Phaeacidiphilus oryzae TH49

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::Smeli:SMc04256
         (361 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  277 bits (708), Expect = 4e-79
 Identities = 162/356 (45%), Positives = 219/356 (61%), Gaps = 12/356 (3%)

Query: 14  GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEPK 73
           G    +D L+L+I  GEFLVL+G SGCGKST L  +AGL DV++G I I +R+VT   PK
Sbjct: 16  GDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPK 75

Query: 74  DRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPSE 133
           DR I MVFQ+YALYP MTV  N+ F LK+A +  AEI  +V+ A++IL +   L RKP  
Sbjct: 76  DRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAAKILDLTEFLDRKPKA 135

Query: 134 LSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVTHD 193
           LSGGQRQRVA+GRA+VR+  VFL DEPLSNLDAKLR   R +I  L + L  T +YVTHD
Sbjct: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITTVYVTHD 195

Query: 194 QIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEPKDGRS 253
           Q+EA+T+ DR+AV+K G++QQ+  P  +Y+ P NLFVAGFIGSP+MN    EV   DG  
Sbjct: 196 QVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLV--EVPITDGG- 252

Query: 254 FVRAGGIAFDVTAYPAHTRLQPGQK-VVLGLRPEHVKVDEARDGEPTHQAV---VDIEEP 309
            V+ G     V+          G K V +G+RPEH+ +    +G    + +   V++ E 
Sbjct: 253 -VKFGESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGGGEDKGLAVTVNVVEE 311

Query: 310 MGADNLLW----LTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENRL 361
           +GAD  ++    +      + VR+ G+     G  +R+    G   +F   +  RL
Sbjct: 312 LGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGETHVFSTSTGKRL 367


Lambda     K      H
   0.320    0.137    0.392 

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: 392
Number of extensions: 17
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: 361
Length of database: 369
Length adjustment: 30
Effective length of query: 331
Effective length of database: 339
Effective search space:   112209
Effective search space used:   112209
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 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