GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Klebsiella michiganensis M5al

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD

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



>FitnessBrowser__Koxy:BWI76_RS03270
          Length = 376

 Score =  333 bits (854), Expect = 4e-96
 Identities = 183/366 (50%), Positives = 241/366 (65%), Gaps = 14/366 (3%)

Query: 1   MTGLLLKDIRKSY-GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59
           M  + L+ I K Y      +HGIDL+I +GEF+VFVGPSGC KST LRMIAGLE+I+GG+
Sbjct: 1   MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60

Query: 60  MFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119
           ++I   +VND+PP  RGIAMVFQ+YALYPH TV+DNMAFG+++ +  K+EI RRV  AA+
Sbjct: 61  IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120

Query: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179
            L++T  L R PK +SGGQRQRVA+GRAI R P VFLFDEPLSNLDA LRV+ R++IA+L
Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180

Query: 180 SERMSD----TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFI 235
              + +     TMIYVTHDQ EA+TL DRI VL+ G+I QV  P +LY  P N FVA FI
Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240

Query: 236 GSPAMNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENG---KTASFGVRPEDLRVTE 292
           GSP++N+I   I    ++  V +A G  + +         G   K   FG+RPE + +  
Sbjct: 241 GSPSINLIDTAIRKNNERLYVEIAPGVEILIPHSKQVLLEGYINKPVCFGIRPEHISLAS 300

Query: 293 ADDFL--FEGTVSIVEALGEVTLLYIEGLVENEPIIAKM--PGIARVGRGDKVRFTADKA 348
            DD L  FEG +++VE +G    LY   +V  + +IA++    I     G  +RF  + A
Sbjct: 301 DDDDLNTFEGVLTVVENMGSEKFLYF--IVGGKELIARVDTQDINPFHIGKTLRFNLNTA 358

Query: 349 KLHLFD 354
             H+FD
Sbjct: 359 FCHVFD 364


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: 398
Number of extensions: 19
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: 362
Length of database: 376
Length adjustment: 30
Effective length of query: 332
Effective length of database: 346
Effective search space:   114872
Effective search space used:   114872
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