GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Klebsiella michiganensis M5al

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate BWI76_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__Koxy:BWI76_RS06690
          Length = 369

 Score =  297 bits (760), Expect = 4e-85
 Identities = 161/316 (50%), Positives = 214/316 (67%), Gaps = 18/316 (5%)

Query: 20  TVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDI 79
           T+ + NL+I DGEF V VGPSGCGKST LRM+AGLE V++G + IGD+ +  V P  R +
Sbjct: 18  TLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEGEVLIGDEVMNDVVPAHRGV 77

Query: 80  AMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGG 139
           AMVFQ+YALYPHMTV ENMG+ LK+    +DEI ++V+  A TL L+  L+RKPK LSGG
Sbjct: 78  AMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVAKTLQLSHLLDRKPKQLSGG 137

Query: 140 QRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEA 199
           QRQRVA+GRAIVRNP+VF+ DEPLSNLDA+LRV+ R  IA L  +L  T VYVTHDQ EA
Sbjct: 138 QRQRVAIGRAIVRNPRVFMFDEPLSNLDAELRVEMRLHIAKLHHELKTTMVYVTHDQVEA 197

Query: 200 LTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHAR 259
           +T+ D+I V+  G ++Q+G+P  LY  P N FVAGFIGSP MN    +V       G   
Sbjct: 198 MTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPKMNFLPATVTAWQ--PGQLS 255

Query: 260 IKLSPE---TLAAMTP--EDNGRITIGFRPEALEIIPEGESTDLSIPIKLDF----VEEL 310
           +K++ +   TL   T   +    +T+G RPE L       STD++I   ++F    VE L
Sbjct: 256 VKMAQDHNLTLNITTSPLQPGAAVTLGIRPEHL-------STDVNIGTVVEFQCEVVERL 308

Query: 311 GSDSFLYGKLVGEGDL 326
           G++++L+G+  G  ++
Sbjct: 309 GNNTYLFGQCYGHDNV 324


Lambda     K      H
   0.316    0.135    0.380 

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: 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: 376
Length of database: 369
Length adjustment: 30
Effective length of query: 346
Effective length of database: 339
Effective search space:   117294
Effective search space used:   117294
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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