GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Pseudomonas putida KT2440

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit

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



>FitnessBrowser__Putida:PP_1018
          Length = 384

 Score =  278 bits (711), Expect = 2e-79
 Identities = 164/368 (44%), Positives = 226/368 (61%), Gaps = 15/368 (4%)

Query: 1   MTGLLLKDIRKSYGA--VDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGG 58
           M  L L+++ K+YG+   D +  I L IK+GEF++ VGPSGCGKSTL+  IAGLE+ITGG
Sbjct: 1   MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60

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

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

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

Query: 239 AMNVIPATITATGQQTAVSLAGGKS---VTLDVPTNASENGKTASFGVRPEDLRVTEADD 295
            MN IP  +     +    L  G++   + L    +A E G+    G+RPE + +  AD 
Sbjct: 240 PMNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALE-GREIILGIRPEQIALGAADG 298

Query: 296 F---LFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIA-RVGRGDKVRFTADKAKLH 351
                    V + E  G   L+++  L + +      P +A RV  GD +    D A++ 
Sbjct: 299 NGLPAIRAEVQVTEPTGPDLLVFVT-LNQTKVCCRLAPDVACRV--GDTLNLQFDPARVL 355

Query: 352 LFD-TNGQ 358
           LFD  NG+
Sbjct: 356 LFDAANGE 363


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: 366
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: 362
Length of database: 384
Length adjustment: 30
Effective length of query: 332
Effective length of database: 354
Effective search space:   117528
Effective search space used:   117528
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