GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Keio:17340 b3270 putative transport system
           permease protein (VIMSS)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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