GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SM_b21106 in Phaeobacter inhibens BS107

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate GFF3855 PGA1_78p00190 sn-glycerol-3-phosphate import ATP-binding protein UgbC

Query= reanno::Smeli:SM_b21106
         (365 letters)



>lcl|FitnessBrowser__Phaeo:GFF3855 PGA1_78p00190
           sn-glycerol-3-phosphate import ATP-binding protein UgbC
          Length = 361

 Score =  307 bits (787), Expect = 3e-88
 Identities = 175/359 (48%), Positives = 234/359 (65%), Gaps = 12/359 (3%)

Query: 4   VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63
           V ++ L   +G L+V+H ++L+++  EF+ L+G SGCGKST L  IAGL ++S G I I 
Sbjct: 8   VEIRDLDLHFGELQVLHQLNLDIEQGEFLVLLGSSGCGKSTLLNCIAGLLDISDGQIFIQ 67

Query: 64  GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDL 123
           G+ V    P  R I MVFQSYALYP MTV  N+ F LK A  P  EI  RVA AA +L +
Sbjct: 68  GQNVTWAEPSERGIGMVFQSYALYPQMTVEGNLSFGLKNARLPKAEIAKRVARAAEVLQI 127

Query: 124 AHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARM 183
             LL+R+P+ LSGGQRQRVA+GRA+VR  DVFLFDEPLSNLDAKLR  +R E+K+LH ++
Sbjct: 128 EPLLKRKPAALSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRADLRVELKRLHQQL 187

Query: 184 QATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEE 243
             TMIYVTHDQVEAMTL+DRI IM+ G I Q+ +P++++ RP   +VAGFIGSP MN+ E
Sbjct: 188 ANTMIYVTHDQVEAMTLADRIAIMKGGRIMQLSSPDEIYNRPQNLYVAGFIGSPAMNLIE 247

Query: 244 AVLTDGKLAFASGATLPLPPR---FRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAVH 300
            VL DG   F +G +L LP +   +R+    G  V  G+RP+ +  +G  +   DA A  
Sbjct: 248 GVLIDG--VFHAG-SLALPMQRYDYRNGPHHGAAV-IGIRPEHIL-TGEQITRADATA-- 300

Query: 301 EIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLFDGET 359
             E+ V + E LG++TLV+     ++   RM     +  G+ + + FD  RA LFD  T
Sbjct: 301 --EVLVDLVEGLGSDTLVYATHGAQNLRLRMDGASRVSAGDRLRIGFDTGRASLFDPNT 357


Lambda     K      H
   0.320    0.137    0.397 

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: 353
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: 365
Length of database: 361
Length adjustment: 29
Effective length of query: 336
Effective length of database: 332
Effective search space:   111552
Effective search space used:   111552
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 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