GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltK in Phaeobacter inhibens BS107

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate GFF3909 PGA1_65p00120 putative amino-acid ABC transporter, permease protein

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



>FitnessBrowser__Phaeo:GFF3909
          Length = 224

 Score =  112 bits (280), Expect = 6e-30
 Identities = 69/218 (31%), Positives = 126/218 (57%), Gaps = 8/218 (3%)

Query: 3   LDFSGVVQAVPGMWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYF 62
           LD + ++  VP + + + +TL + V+ +V  ++L +LLA+ R+    +L  +   ++++F
Sbjct: 4   LDIAYMLGLVPVLLSYVPLTLFMAVVAMVLALVLASLLAVERVLRIPVLDQLVVLFISFF 63

Query: 63  RSIPLLLVITWFYLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQSIP 122
           R  PLL+ +  FY  +P VL  +T     I   ++ I+   +  AAY  E +RA +  + 
Sbjct: 64  RGTPLLVQLFLFYYGLPQVLSVLT----QINGVSAAIMGLTLHFAAYMAESIRAAILGVD 119

Query: 123 KGQMGAAKALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNAT 182
           + Q  AA+++GM  GQMMR I+LPQA R   P L+   I + + TSL +T+G+ + + AT
Sbjct: 120 RSQWEAAQSIGMTRGQMMRRIVLPQAARIAAPTLVNYFIDMIKGTSLAFTLGVTEMMGAT 179

Query: 183 R--ASGDIIGRANEFLIIAGLVYFTISFAASRLVKRLQ 218
           +  A+G  +     FL++A ++Y+ +  A S + +RL+
Sbjct: 180 QKEAAGSFL-YFEAFLVVA-VIYWILVEALSLVQRRLE 215


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: 117
Number of extensions: 6
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: 223
Length of database: 224
Length adjustment: 22
Effective length of query: 201
Effective length of database: 202
Effective search space:    40602
Effective search space used:    40602
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: 46 (22.3 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