GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Synechococcus elongatus PCC 7942

Align PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine

Query= TCDB::Q88NY4
         (223 letters)



>FitnessBrowser__SynE:Synpcc7942_0248
          Length = 396

 Score =  128 bits (321), Expect = 2e-34
 Identities = 73/210 (34%), Positives = 121/210 (57%), Gaps = 7/210 (3%)

Query: 16  WEGMVMTLKLMVMGVIGGIVLGTILALMRLSSSKLLSNLAGAYVNYFRSIPLLLVITWFY 75
           W G+++TL   ++ ++  + LG +LAL R SS   +  L+  Y+  FR +PL+ ++ +  
Sbjct: 188 WSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQ 247

Query: 76  LAVPFVLRWITGEDTPVGAFTSCVVAFMMFEAAYFCEIVRAGVQSISKGQMGAAQALGMN 135
           + VP +L      +  +      +V   +F +AY  E VR G+Q+I +GQ  AA ALG+N
Sbjct: 248 VMVPLML----DSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLN 303

Query: 136 YAQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNSARS---NGDIIGRS 192
             QT R I+LPQA R   P ++   + L QDT+L+  VGL++ L  +RS   N   +GR 
Sbjct: 304 LFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRY 363

Query: 193 HEFLIFAGVVYFLISFSASWLVKRLQKRIS 222
            E  +F GV+Y+L  +  + L +RL++R++
Sbjct: 364 AEVYLFLGVLYWLCCYGLAQLSRRLEQRLT 393


Lambda     K      H
   0.330    0.141    0.417 

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: 296
Number of extensions: 10
Number of successful extensions: 3
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: 396
Length adjustment: 26
Effective length of query: 197
Effective length of database: 370
Effective search space:    72890
Effective search space used:    72890
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.

Links

Downloads

Related tools

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