GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Phaeobacter inhibens BS107

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 GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__Phaeo:GFF196
          Length = 432

 Score =  291 bits (746), Expect = 2e-83
 Identities = 171/434 (39%), Positives = 246/434 (56%), Gaps = 72/434 (16%)

Query: 8   FVRTSILAAEPPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAV 67
           FVR + +   PPP  E G   WIR NL ++  + ILT+ ALALI   +   + WL +  V
Sbjct: 11  FVRETQIPPAPPPGRETGVYKWIRENLFSSVPNSILTLAALALIYALLSSTLPWL-LNGV 69

Query: 68  WSGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFG-RYPLGERWRPAIVGILFIL 126
           W+      C   L      DG  GAC++ ++ +++Q ++G +YP  E WRP +  +L ++
Sbjct: 70  WTTNSLAECREVL------DGKLGACFSVLTERWNQLLYGFKYPGTEYWRPNLALVLLLV 123

Query: 127 LLVPMLIPSAPRKGLNAILLF-AVLPVIAFWLLHGG------------------------ 161
            L P+L    PRK    +L F A+ P +AFWL+ GG                        
Sbjct: 124 ALAPVLFFDLPRK----LLAFTAIYPFLAFWLIWGGSILVPIVALLGFVAAGFVFQKFGK 179

Query: 162 -------FGLEVVETPLW-------------------------GGLMVTLVLSFVGIAVS 189
                  FG  V    +W                         GG M+ ++L    +++S
Sbjct: 180 GSFALGFFGAIVAAVVVWNIGGFLIPEGASDNAMLSAVPSRDLGGFMLNMMLGVTCVSLS 239

Query: 190 LPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLR 249
           +P+GI LALGR+S MP+I+ +CV FIE +RGVPLIT+LF+ASVML  F P    VD  LR
Sbjct: 240 VPLGIALALGRQSNMPLIKWICVVFIEFVRGVPLITLLFVASVMLSYFFPPDATVDLFLR 299

Query: 250 ALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIV 309
            +I +++F++AY+AEVIRGGL A+PKGQ+E ADSLGL Y Q  RLII+PQA+K+ IP IV
Sbjct: 300 VVIMITLFSAAYIAEVIRGGLAALPKGQYEAADSLGLDYPQAMRLIILPQALKISIPGIV 359

Query: 310 NTFIGTFKDTSLVTIIGMFDLLGIVK-LNFSDANWASAVTPITGLIFAGFIFWLFCFGMS 368
           N  +G FKDT+LV++I MFDL+G+++    +   W      + G  FA F+F++ C+G+S
Sbjct: 360 NVAVGLFKDTTLVSVISMFDLVGMIRGPILASTEWNGVYWELLG--FAAFLFFIVCYGIS 417

Query: 369 RYSGFMERHLDTGH 382
           +YS ++ER L T H
Sbjct: 418 QYSQWLERRLATDH 431


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: 527
Number of extensions: 38
Number of successful extensions: 6
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: 384
Length of database: 432
Length adjustment: 31
Effective length of query: 353
Effective length of database: 401
Effective search space:   141553
Effective search space used:   141553
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