GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Acidovorax sp. GW101-3H11

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4785
          Length = 334

 Score =  323 bits (829), Expect = 3e-93
 Identities = 174/331 (52%), Positives = 226/331 (68%), Gaps = 7/331 (2%)

Query: 17  VGSLQLKTIRKAFG----SHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDAT 72
           + SL L+ I K +G    +++V+ G++ +VKDGEFV+ VGPSGCGKSTLLR +AGLE+ +
Sbjct: 1   MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60

Query: 73  SGSVQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAK 132
            G ++I    V  + PA+R IAMVFQ+YALYPH+T  +NM  GLK A VPK EI+ +V K
Sbjct: 61  GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120

Query: 133 AAGMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEI 192
           AA +L L   L R+P ELSGGQRQRVA+GRAIVR+P++FLFDEPLSNLDA LR  TRLEI
Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180

Query: 193 ARLHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGS 252
            +LHR L  T ++VTHDQVEAMTLA +++V+NAG +EQ G+P E+Y+ PA  FVA FIGS
Sbjct: 181 QKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIGS 240

Query: 253 PQMNFIEAAKLGDGEAKTIGIRPEHIGLSRESGDWKGKVIHVEHLGADTIIYIESETVGL 312
           P MN ++ A  G      +GIRPEH+ +  E   W   V  VE LGA+ +IY       +
Sbjct: 241 PPMNLLKNAP-GAQPGTILGIRPEHLDVRSEG--WAVTVETVELLGAERLIYGRINGEQV 297

Query: 313 LTVRLFGEHRYATDDIVHATPVIGSMHRFDA 343
           +     G H    D ++H  P    +H FDA
Sbjct: 298 IVRVEEGTHSPEPDSVIHVQPRADRLHAFDA 328


Lambda     K      H
   0.320    0.137    0.393 

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: 317
Number of extensions: 15
Number of successful extensions: 4
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: 352
Length of database: 334
Length adjustment: 29
Effective length of query: 323
Effective length of database: 305
Effective search space:    98515
Effective search space used:    98515
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