GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocE in Corynebacterium deserti GIMN1.010

Align Amino-acid permease RocE (characterized)
to candidate WP_053544618.1 CDES_RS05420 amino acid permease

Query= SwissProt::P39137
         (467 letters)



>NCBI__GCF_001277995.1:WP_053544618.1
          Length = 468

 Score =  266 bits (679), Expect = 1e-75
 Identities = 144/438 (32%), Positives = 234/438 (53%), Gaps = 4/438 (0%)

Query: 15  MKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGELAVAF 74
           +++RH+  I+LG  IGTG F G+   I  AGP   +L YL+GG +++  +  LGE++V  
Sbjct: 14  LRARHIHFIALGSAIGTGLFYGSAGAIQAAGP-SVLLVYLLGGAVVYFMLRALGEMSVHH 72

Query: 75  PVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWIWCLV 134
           PV GSF  Y    +    G+  GW++     + C  +  + G  M  WFP    W+W   
Sbjct: 73  PVRGSFAVYTRAHLGGWAGYITGWMFAFEMLIVCLADLTAIGIYMNFWFPDTPQWVWVAA 132

Query: 135 FAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAPFLTHF 194
              ++   N  + + F E E  F+ +K+  ++  I+ GGAA+         E A     +
Sbjct: 133 TLLIVGGANLASVRWFGELEVVFTIVKVTAVIAMIV-GGAAILAFGLGSNAEVAGISNLW 191

Query: 195 YEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRTLVFFV 254
              G FPNGI+ M+   I V FAF GTE+IGVA  E+E+PEK+IP+++     R L+F+V
Sbjct: 192 EHGGFFPNGIEGMIAAFILVLFAFGGTEIIGVAGSEAEEPEKSIPKAVNTVPVRILLFYV 251

Query: 255 LSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGLYASTRI 314
            +I+VI  + PW      ESPFV +F+ +G+ +AA ++N V++ A LS  N+ L+ + R+
Sbjct: 252 GAILVILALNPWPSITGEESPFVQIFDTLGVNWAAGLLNLVVITAALSAINADLFGAGRV 311

Query: 315 LYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLSLAGMSA 374
           L  +A E  A KA+GK  + GVP+ + I+ + V  + ++      E V+ ++ SLA  + 
Sbjct: 312 LTGLAKENLAPKAMGKIAKNGVPIMTTIIMIIVLIVGVILNAVLPERVFEIVASLATFAT 371

Query: 375 QVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISLAFDPEQR 434
              W+ I L+Q+  RR+   E  ++E LKF  P YP      +         + +     
Sbjct: 372 VYVWLMILLAQVGSRRRMSAE--EVETLKFPVPFYPFGQYFAILFIAFTFGIMVWYENYH 429

Query: 435 IALYCGVPFMIICYIIYH 452
           + L  GV F+++  I+Y+
Sbjct: 430 LPLAVGVGFLVLMTILYY 447


Lambda     K      H
   0.329    0.142    0.438 

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: 539
Number of extensions: 34
Number of successful extensions: 4
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: 467
Length of database: 468
Length adjustment: 33
Effective length of query: 434
Effective length of database: 435
Effective search space:   188790
Effective search space used:   188790
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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