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_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein

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



>FitnessBrowser__Koxy:BWI76_RS06690
          Length = 369

 Score =  343 bits (880), Expect = 4e-99
 Identities = 182/357 (50%), Positives = 244/357 (68%), Gaps = 3/357 (0%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M+ + L+++ K +G+   +H ++LDI++GEF VFVGPSGCGKSTLLRMIAGLEE++ G++
Sbjct: 1   MSNIRLRNVTKRFGSTVTLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEGEV 60

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
            I  E +NDV P+ RG+AMVFQSYALYPHMTV +NM +G+++ +  K+EI R+V   A  
Sbjct: 61  LIGDEVMNDVVPAHRGVAMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVAKT 120

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           LQL+  LDR PK LSGGQRQRVAIGRAI RNP+VF+FDEPLSNLDA LRV  R+ IAKL 
Sbjct: 121 LQLSHLLDRKPKQLSGGQRQRVAIGRAIVRNPRVFMFDEPLSNLDAELRVEMRLHIAKLH 180

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
             +  TTM+YVTHDQVEAMTLAD+IVV++ G +EQ+G+P+ LY  P N FVA FIGSP M
Sbjct: 181 HELK-TTMVYVTHDQVEAMTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPKM 239

Query: 241 NVIPATITA-TGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFE 299
           N +PAT+TA    Q +V +A   ++TL++ T+  + G   + G+RPE L        + E
Sbjct: 240 NFLPATVTAWQPGQLSVKMAQDHNLTLNITTSPLQPGAAVTLGIRPEHLSTDVNIGTVVE 299

Query: 300 GTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTN 356
               +VE LG  T L+ +    ++ +   +PG        K+    D     +FD N
Sbjct: 300 FQCEVVERLGNNTYLFGQ-CYGHDNVKILLPGDVHFRPWQKISVAFDDRYCMVFDEN 355


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: 347
Number of extensions: 11
Number of successful extensions: 3
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: 369
Length adjustment: 30
Effective length of query: 332
Effective length of database: 339
Effective search space:   112548
Effective search space used:   112548
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