GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate H281DRAFT_05887 H281DRAFT_05887 carbohydrate ABC transporter ATP-binding protein, CUT1 family

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>FitnessBrowser__Burk376:H281DRAFT_05887
          Length = 345

 Score =  184 bits (467), Expect = 3e-51
 Identities = 123/356 (34%), Positives = 182/356 (51%), Gaps = 26/356 (7%)

Query: 2   QLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTV 61
           ++ L ++SK+ G    + D+S+ +  G   VLLG + AGKT+ +R++AGL+ P AG V +
Sbjct: 3   EIQLRNVSKRFGDIAAVDDISIDVADGEFVVLLGPSGAGKTTTLRLIAGLERPDAGDVLI 62

Query: 62  DGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKL----RGEKNIDARVREIASR 117
           DG   TG+   DR+VA ++QQ+  YP + V  N+A PL+       E ++ ARV  +A  
Sbjct: 63  DGTIATGVHPSDRDVAFIFQQYSLYPHLTVFGNLAFPLRSPRRRSSEADVRARVHAVAEM 122

Query: 118 LHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLF 177
           LH++  LD     LSGG+ QRVA+ RAL +     L+DEPL +LD KLREELR EL +L 
Sbjct: 123 LHMEAKLDNMATHLSGGEMQRVAIGRALVRQPKAFLMDEPLSSLDAKLREELRIELKRLH 182

Query: 178 AAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMN 237
               +T+VY T +  EA  L     +LD G+L+Q G   EV+  P SL  A+    PP+N
Sbjct: 183 RTIGATIVYVTHDQVEATTLADRIGILDHGRLVQLGTPREVYGNPVSLSAAQRLGSPPIN 242

Query: 238 LMAASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGV---- 293
           L+  +              +  +P G A     TVG+R   + +H  P +   +G     
Sbjct: 243 LLPPTLFD-----------SAHMPAGTA-----TVGIRPEDIVLH-DPAEGHASGAQDAL 285

Query: 294 -VELAEISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGR 348
            + + E S     +        +VA       F  G  + + L P     F ADGR
Sbjct: 286 DLTVLEYSPLRHLLILDRAGTAVVATTVTERSFSPGQRVGVSLPPRSLLYFHADGR 341


Lambda     K      H
   0.318    0.133    0.375 

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: 283
Number of extensions: 14
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: 363
Length of database: 345
Length adjustment: 29
Effective length of query: 334
Effective length of database: 316
Effective search space:   105544
Effective search space used:   105544
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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