GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Klebsiella michiganensis M5al

Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate BWI76_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_792
         (358 letters)



>FitnessBrowser__Koxy:BWI76_RS06690
          Length = 369

 Score =  202 bits (515), Expect = 9e-57
 Identities = 117/295 (39%), Positives = 181/295 (61%), Gaps = 17/295 (5%)

Query: 20  SDYALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQE 79
           S   L  + ++ EDG     +GPSGCGK+T+L +++GL   S G+VL     +    P  
Sbjct: 15  STVTLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEGEVLIGDEVMNDVVPAH 74

Query: 80  RNIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGL 139
           R +A VFQ   +Y  MTVAEN+ + L+  KVP+ +I+++V ++A+ L++S  L+++   L
Sbjct: 75  RGVAMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVAKTLQLSHLLDRKPKQL 134

Query: 140 AADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHD 199
           +   +Q++++GR +VR +    +FDEPL+ +D  L+ ++R  + ++HHELK T++YVTHD
Sbjct: 135 SGGQRQRVAIGRAIVR-NPRVFMFDEPLSNLDAELRVEMRLHIAKLHHELKTTMVYVTHD 193

Query: 200 QVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLP----AHRDGE 255
           QVEA+T AD++VVM  GK  Q+GS  +L+  P + FV  FIGSP MNFLP    A + G+
Sbjct: 194 QVEAMTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPKMNFLPATVTAWQPGQ 253

Query: 256 NLSV---AGHRLASPVGRA--LPAGALQVGIRPEYLALAQPQQAGALPGTVVQVQ 305
            LSV     H L   +  +   P  A+ +GIRPE+L+           GTVV+ Q
Sbjct: 254 -LSVKMAQDHNLTLNITTSPLQPGAAVTLGIRPEHLS------TDVNIGTVVEFQ 301


Lambda     K      H
   0.320    0.136    0.395 

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: 317
Number of extensions: 16
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: 358
Length of database: 369
Length adjustment: 29
Effective length of query: 329
Effective length of database: 340
Effective search space:   111860
Effective search space used:   111860
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