GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Phaeacidiphilus oryzae TH49

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

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



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  172 bits (435), Expect = 2e-47
 Identities = 118/357 (33%), Positives = 186/357 (52%), Gaps = 16/357 (4%)

Query: 3   LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62
           L L  ++KK G+ T +  + L +  G+   LLGA+  GKT+ +R+++GL+APTAGR+ + 
Sbjct: 19  LRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLG 78

Query: 63  GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDARVREIASRLHIDM 122
            +DVT      R V  V+Q +  +P + +  N+A  L+ RG +++   V ++   + +  
Sbjct: 79  DQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGIRSVKKPVEDMLDLVELGH 138

Query: 123 FLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQS 182
              R P +LSGGQQQR+ALARAL     ++LLDEPL  LD KLR +++ EL ++      
Sbjct: 139 LARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEVGL 198

Query: 183 TVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMAA- 241
           T V+ T +  EA+ +    AV++ G++ Q G  AE++  PN+  VA        NL+A  
Sbjct: 199 TFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQ--SNLIAGT 256

Query: 242 --SATAQGVRLQG-GAELTLPLPQGAATAAGLTVGVRASALRVHARPGDV-----SVAGV 293
             S +   V++   G  L LP  +   T+  + +GVR   +R+     +V      + G 
Sbjct: 257 VESVSGDVVQVAAHGRSLALPAARCRTTSGPVILGVRPEKVRIAKTEAEVPSGANHLTGK 316

Query: 294 VELAEISGSDTFVHASTPWGDLVA---QLTGVHYFELGTAITLHLDPAQAYVFGADG 347
           V  A   G  T      P G+ +A   Q TG      G  + +H DP+Q   FG DG
Sbjct: 317 VTDASFIGVSTQYLVELPSGEELAVFEQNTGQEIQRPGAEVVVHWDPSQG--FGLDG 371


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: 301
Number of extensions: 13
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: 386
Length adjustment: 30
Effective length of query: 333
Effective length of database: 356
Effective search space:   118548
Effective search space used:   118548
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: 50 (23.9 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