GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Rhodobacter johrii JA192

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC

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



>NCBI__GCF_003046325.1:WP_069331237.1
          Length = 349

 Score =  341 bits (874), Expect = 2e-98
 Identities = 188/364 (51%), Positives = 239/364 (65%), Gaps = 16/364 (4%)

Query: 1   MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60
           MA ++L+ + K Y  LEV+HG+DLE+ D EF+ +VGPSGCGKST LRM+AGLEE++ G I
Sbjct: 1   MAEISLRDVRKSYSGLEVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAGEI 60

Query: 61  EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120
            IGGR VN L PR R+I+MVFQ+YALYPHMTV ENM + L+IA     EI+ RVA +A +
Sbjct: 61  AIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSAKM 120

Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180
           L+L  LL+R+P QLSGGQRQRVAMGRA+VR P  FL DEPLSNLDAKLR Q+R +IK+L 
Sbjct: 121 LELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKELQ 180

Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240
             ++ T IYVTHDQVEAMTL+DR+V+M  G  EQ+ TP +++ RPAT FVAGFIGSP MN
Sbjct: 181 RTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPAMN 240

Query: 241 MEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAVH 300
           M  A      L  A G  L +P         G+ +  G+RP+ ++P+G            
Sbjct: 241 MLPARGLGDALEVA-GQRLAVP------APAGRDLILGIRPEHLHPAG--------PEEP 285

Query: 301 EIELPVTITEPLGNETLVFTQF-NGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLFDGET 359
             EL V   E LG +        +G D V R     P+R  + + ++ D A  HLFD  T
Sbjct: 286 GFELHVQAVEWLGADAFAHGSLADGTDLVLRTPGKAPVRERDRLKVAPDAAALHLFDAGT 345

Query: 360 GRAL 363
           GR L
Sbjct: 346 GRRL 349


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: 415
Number of extensions: 27
Number of successful extensions: 3
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: 349
Length adjustment: 29
Effective length of query: 336
Effective length of database: 320
Effective search space:   107520
Effective search space used:   107520
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 24 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