GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF3855
          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:

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