GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Escherichia coli BW25113

Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate 17340 b3270 putative transport system permease protein (VIMSS)

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__Keio:17340
          Length = 367

 Score =  363 bits (931), Expect = e-105
 Identities = 184/375 (49%), Positives = 250/375 (66%), Gaps = 17/375 (4%)

Query: 11  TSILAAEPPPPGERG---AVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAV 67
           T +L + PP P       A+ W+R+NL ++  + +LTI  + L+   +P L+NW F+QA 
Sbjct: 2   TKVLLSHPPRPASHNSSRAMVWVRKNLFSSWSNSLLTIGCIWLMWELIPPLLNWAFLQAN 61

Query: 68  WSGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILL 127
           W G  R  C             +GACW FI  ++ QF++G YP  +RWR  +  ++ ++ 
Sbjct: 62  WVGSTRADCTK-----------AGACWVFIHERFGQFMYGLYPHDQRWRINLALLIGLVS 110

Query: 128 LVPMLIPSAPRKGLNAILLFAVLPVIAFWLLHGGF-GLEVVETPLWGGLMVTLVLSFVGI 186
           + PM     P +G        + P+I +WL++GGF  LE VET  WGGL +TL+++ VGI
Sbjct: 111 IAPMFWKILPHRGRYIAAWAVIYPLIVWWLMYGGFFALERVETRQWGGLTLTLIIASVGI 170

Query: 187 AVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDK 246
           A +LP GILLALGRRS MP++R+L V FIE  RGVPLITVLFM+SVMLPLF+  G ++DK
Sbjct: 171 AGALPWGILLALGRRSHMPIVRILSVIFIEFWRGVPLITVLFMSSVMLPLFMAEGTSIDK 230

Query: 247 LLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIP 306
           L+RAL+GV +F SAY+AEV+RGGLQA+PKGQ+E A+SL LGYW+   L+I+PQA+KLVIP
Sbjct: 231 LIRALVGVILFQSAYVAEVVRGGLQALPKGQYEAAESLALGYWKTQGLVILPQALKLVIP 290

Query: 307 SIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFG 366
            +VNT I  FKDTSLV IIG+FDL   V+    D  W    T   G +FA  I+W+FCF 
Sbjct: 291 GLVNTIIALFKDTSLVIIIGLFDLFSSVQQATVDPAWLGMST--EGYVFAALIYWIFCFS 348

Query: 367 MSRYSGFMERHLDTG 381
           MSRYS ++E+  +TG
Sbjct: 349 MSRYSQYLEKRFNTG 363


Lambda     K      H
   0.330    0.145    0.469 

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: 564
Number of extensions: 26
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: 384
Length of database: 367
Length adjustment: 30
Effective length of query: 354
Effective length of database: 337
Effective search space:   119298
Effective search space used:   119298
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: 50 (23.9 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