GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltK in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate H281DRAFT_02614 H281DRAFT_02614 L-glutamine ABC transporter membrane protein

Query= reanno::pseudo3_N2E3:AO353_16280
         (223 letters)



>FitnessBrowser__Burk376:H281DRAFT_02614
          Length = 218

 Score =  117 bits (294), Expect = 1e-31
 Identities = 69/226 (30%), Positives = 119/226 (52%), Gaps = 12/226 (5%)

Query: 1   MDLDFSGVVQAVPGMWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVN 60
           M  D S +V AVP + +G  +T+ +T+ G+ GG+ +G +  LMR   + L   IA  Y+ 
Sbjct: 1   MQFDLSVIVDAVPALMHGARLTVLITIAGLAGGMFVGLVFGLMRAYGNTLCQKIAFTYIE 60

Query: 61  YFRSIPLLLVITWFYLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQS 120
           + R  P+++ + + Y A+P ++         + A T+ IV+ ++   AY  EIVR    S
Sbjct: 61  FVRGTPIVVQVMFIYFALPLLMH------VRVDAMTAAIVSIIINSGAYIAEIVRGAFLS 114

Query: 121 IPKGQMGAAKALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLN 180
           +P+G   A  ALGM   +++  ++ P A R+MTP L  Q I+  +DTSL   +G+ +   
Sbjct: 115 VPRGLKEAGLALGMPGWRVLAFVVGPVALRRMTPALGNQFIVSLKDTSLFIVIGVGEL-- 172

Query: 181 ATRASGDIIG---RANEFLIIAGLVYFTISFAASRLVKRLQKRFAV 223
            TR   +I+    RA E      L+Y  +  A S  ++ +++R  +
Sbjct: 173 -TRQGQEIMASNFRAVEIWTAVALIYLCMIGALSFGLRTMERRMRI 217


Lambda     K      H
   0.331    0.143    0.425 

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: 122
Number of extensions: 5
Number of successful extensions: 1
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: 223
Length of database: 218
Length adjustment: 22
Effective length of query: 201
Effective length of database: 196
Effective search space:    39396
Effective search space used:    39396
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 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