GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacF in Klebsiella michiganensis M5al

Align LacF, component of Lactose porter (characterized)
to candidate BWI76_RS23380 BWI76_RS23380 sugar ABC transporter permease

Query= TCDB::P29823
         (298 letters)



>FitnessBrowser__Koxy:BWI76_RS23380
          Length = 296

 Score =  158 bits (399), Expect = 2e-43
 Identities = 99/284 (34%), Positives = 164/284 (57%), Gaps = 14/284 (4%)

Query: 17  GWLFVAPAIALISVFMLYPILRSLVLSLYTGRGMMLK--FSGTGNL-VRLWNDPVFWQAL 73
           G  +++P I  + VF  +P + S  LS +T   +M    F+G  N    L  D +FW+++
Sbjct: 8   GLAWISPYIIGLIVFTAFPFVSSFFLS-FTEYDLMSPPVFNGIENYRYMLTEDGLFWKSM 66

Query: 74  QNTVIFFVVQVPIMITMALILAAMLNNPKLRYSGLFRTMIFLPCV-SSLVAYSILFKSMF 132
             T  +  + +P+ +  AL +A +LN  KLR  G FRT  ++P +  S VA ++L++++F
Sbjct: 67  GVTFAYVFLTIPLKLAFALGIAFVLNF-KLRGIGFFRTAYYIPSILGSSVAIAVLWRALF 125

Query: 133 SLDGVVNNTLLAIGIIG-EPIGWLTDPFWAKVLIIIAITWRWTGYNMIFYLAALQNIDRS 191
           ++DG++N+    IG++G +P+ WL +P  A + + +   W++ G  M+ +LAALQN+ +S
Sbjct: 126 AIDGLLNSF---IGVLGFDPVNWLGEPSLALMSVTLLRVWQF-GSAMVIFLAALQNVPQS 181

Query: 192 IYEAAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTLQLFDEVYNFTEGTGGPANST 251
            YEAA IDG   W  F  +T+P++ PVI F  I  T    Q F   Y  T   GGP  ST
Sbjct: 182 QYEAAMIDGASKWQMFMKVTVPLITPVIFFNFIMQTTQAFQEFTGPYVIT--GGGPTYST 239

Query: 252 LTLSLYIYNLTFRFMPSFSYAATVSYVIVLMVAVLSFLQFYAAR 295
              SLYIY+  F++     Y A +++V+ L+VAV + + F +++
Sbjct: 240 YLFSLYIYDTAFKYF-DMGYGAALAWVLFLVVAVFAAIAFKSSK 282


Lambda     K      H
   0.329    0.141    0.435 

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: 299
Number of extensions: 21
Number of successful extensions: 6
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: 298
Length of database: 296
Length adjustment: 26
Effective length of query: 272
Effective length of database: 270
Effective search space:    73440
Effective search space used:    73440
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