GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Pseudomonas simiae WCS417

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__WCS417:GFF4321
          Length = 386

 Score =  281 bits (720), Expect = 2e-80
 Identities = 161/365 (44%), Positives = 227/365 (62%), Gaps = 14/365 (3%)

Query: 1   MTGLLLKDIRKSYGA--VDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGG 58
           M  L L+++ K+YGA   D +  I+L IKEGEF++ VGPSGCGKSTL+  IAGLE ITGG
Sbjct: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60

Query: 59  DMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAA 118
            + I  + V+ + P  R IAMVFQSYALYP M+V +N+ FG++I +  + +ID  V   A
Sbjct: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120

Query: 119 DMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAK 178
            +LQ+   L+R P  LSGGQ+QRVA+GRA+ R PK++LFDEPLSNLDA LRV  R E+  
Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 179 LSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSP 238
           + +R+  TT +YVTHDQ+EAMTL D++ V+  G I+Q G P E+Y  PAN FVA FIGSP
Sbjct: 181 MHQRLK-TTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSP 239

Query: 239 AMNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENG---KTASFGVRPEDLRVTEADD 295
            MN +P  +     +    L  G++   ++  N +E G   +    G+RPE + +   + 
Sbjct: 240 PMNFVPLRLQRKDGRLVALLDSGQA-RCELALNTTEAGLEDRDVILGLRPEQIMLAAGEG 298

Query: 296 ---FLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIA-RVGRGDKVRFTADKAKLH 351
                    V + E  G  TL++++ L + +      P +A +VG    ++F  D +K+ 
Sbjct: 299 DSASSIRAEVQVTEPTGPDTLVFVQ-LNDTKVCCRLAPDVAPQVGETLTLQF--DPSKVL 355

Query: 352 LFDTN 356
           LFD N
Sbjct: 356 LFDAN 360


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: 355
Number of extensions: 16
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: 386
Length adjustment: 30
Effective length of query: 332
Effective length of database: 356
Effective search space:   118192
Effective search space used:   118192
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: 50 (23.9 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