GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Synechococcus elongatus PCC 7942

Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine

Query= SwissProt::P0AER5
         (224 letters)



>FitnessBrowser__SynE:Synpcc7942_0247
          Length = 377

 Score = 79.0 bits (193), Expect = 1e-19
 Identities = 55/197 (27%), Positives = 100/197 (50%), Gaps = 16/197 (8%)

Query: 38  GTMLAVMRLSSFAPVAWFAKAYVN------VFRSIPLVMVLL------WFYLIVPGFLQN 85
           G ++ ++ ++    V+W A+   +      ++ +I +V VL+      W   + PG ++ 
Sbjct: 178 GWLVVILAIALVLFVSWLAQRQRSPRDWRWLYGAIAVVTVLMLLTQLSWPQQLQPGQIRG 237

Query: 86  VLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSISRGQSSAALALGMTHWQSMKLI 145
            L LS    +   + ++    +  A+ +EIIR GI S+  GQ  AA ALG+T  Q++  I
Sbjct: 238 GLRLS----LEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQI 293

Query: 146 ILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTASTIGERDGTQVEMILFAGFVY 205
           ++PQA R +VP L +Q +   +++SL   +   D + TA T   + G  VE+ L     Y
Sbjct: 294 VVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTY 353

Query: 206 FVISLSASLLVSYLKRR 222
             I+   S  ++ L++R
Sbjct: 354 LAINAVISAGMNGLQQR 370



 Score = 33.1 bits (74), Expect = 7e-06
 Identities = 17/65 (26%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 16  LLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPLVM-VLLW 74
           L+ GLV +L++    +++  + GT+  V   S    +   ++ YV V R+ PL++ +++W
Sbjct: 82  LVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVW 141

Query: 75  FYLIV 79
           ++ I+
Sbjct: 142 YFPIL 146


Lambda     K      H
   0.330    0.140    0.412 

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: 230
Number of extensions: 16
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 224
Length of database: 377
Length adjustment: 26
Effective length of query: 198
Effective length of database: 351
Effective search space:    69498
Effective search space used:    69498
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 (21.9 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