GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Maltose and D-Trehalose, 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:SMc03065
         (362 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4785
          Length = 334

 Score =  305 bits (780), Expect = 1e-87
 Identities = 178/359 (49%), Positives = 228/359 (63%), Gaps = 37/359 (10%)

Query: 1   MTGLLLKDIRKSYG----AVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEIT 56
           M  L L++I K YG    A  VIHG++ ++K+GEFVV VGPSGCGKSTLLRM+AGLEEI+
Sbjct: 1   MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60

Query: 57  GGDMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRG 116
           GG++ I    VND+ P++R IAMVFQ+YALYPHMT ++NMA+G++IA+  K+EI  RV  
Sbjct: 61  GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120

Query: 117 AADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEI 176
           AA +L+L   L+R P+ LSGGQRQRVA+GRAI R P+VFLFDEPLSNLDA LR  TR+EI
Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180

Query: 177 AKLSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIG 236
            KL   +   T ++VTHDQVEAMTLA R++V++AG++EQ G P E+Y  PA  FVA FIG
Sbjct: 181 QKLHRELG-ITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIG 239

Query: 237 SPAMNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDF 296
           SP MN++     A G Q    L                       G+RPE L V      
Sbjct: 240 SPPMNLLK---NAPGAQPGTIL-----------------------GIRPEHLDVRSEG-- 271

Query: 297 LFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKA-KLHLFD 354
            +  TV  VE LG   L+Y  G +  E +I ++         D V     +A +LH FD
Sbjct: 272 -WAVTVETVELLGAERLIY--GRINGEQVIVRVEEGTHSPEPDSVIHVQPRADRLHAFD 327


Lambda     K      H
   0.320    0.137    0.387 

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: 346
Number of extensions: 11
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: 362
Length of database: 334
Length adjustment: 29
Effective length of query: 333
Effective length of database: 305
Effective search space:   101565
Effective search space used:   101565
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