GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Klebsiella michiganensis M5al

Align MalF, component of Maltose/trehalose porter (characterized)
to candidate BWI76_RS23380 BWI76_RS23380 sugar ABC transporter permease

Query= TCDB::O51924
         (300 letters)



>FitnessBrowser__Koxy:BWI76_RS23380
          Length = 296

 Score =  155 bits (393), Expect = 8e-43
 Identities = 95/283 (33%), Positives = 153/283 (54%), Gaps = 12/283 (4%)

Query: 21  LGYLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFVGLRNYLRVLSARE-FWYS 79
           LG   I P +  ++VF   P + +F++S   +   +    F G+ NY  +L+    FW S
Sbjct: 7   LGLAWISPYIIGLIVFTAFPFVSSFFLSF-TEYDLMSPPVFNGIENYRYMLTEDGLFWKS 65

Query: 80  TFVTVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIIS-ARTWELMY 138
             VT ++ F+++ L+    L  A +LN +L+G G  R    IP  + + ++ A  W  ++
Sbjct: 66  MGVTFAYVFLTIPLKLAFALGIAFVLNFKLRGIGFFRTAYYIPSILGSSVAIAVLWRALF 125

Query: 139 NYSYGLFNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPLMTLLLLAGLQAIPQDLY 198
               GL N  + +LG  PVNWLG P  A  ++ +  VW+    M ++ LA LQ +PQ  Y
Sbjct: 126 AID-GLLNSFIGVLGFDPVNWLGEPSLALMSVTLLRVWQFGSAM-VIFLAALQNVPQSQY 183

Query: 199 EAALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATTSIS 258
           EAA+IDGAS ++ F  +T+PL+ PV+    I++T  A + F   YV+TGGGP  +T   S
Sbjct: 184 EAAMIDGASKWQMFMKVTVPLITPVIFFNFIMQTTQAFQEFTGPYVITGGGPTYSTYLFS 243

Query: 259 L----LAFNYYNLGDYGIGSAISILTFVLVLSFTIVYLKVGRF 297
           L     AF Y+   D G G+A++ + F++V  F  +  K  ++
Sbjct: 244 LYIYDTAFKYF---DMGYGAALAWVLFLVVAVFAAIAFKSSKY 283


Lambda     K      H
   0.329    0.145    0.436 

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: 284
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: 300
Length of database: 296
Length adjustment: 26
Effective length of query: 274
Effective length of database: 270
Effective search space:    73980
Effective search space used:    73980
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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