GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Dinoroseobacter shibae DFL-12

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 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__Dino:3606890
          Length = 432

 Score =  302 bits (773), Expect = 1e-86
 Identities = 178/436 (40%), Positives = 236/436 (54%), Gaps = 65/436 (14%)

Query: 4   ADKPFVRTSILAAEPPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLF 63
           A   FVRT  +   PPP  E G V W+R NL  +    ILT+L  A I W    L+ W+F
Sbjct: 6   ASAAFVRTEEIPPSPPPVSEVGIVNWLRSNLFYSIPSSILTLLTAAFIYWLSSILMPWMF 65

Query: 64  IQAVWSGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGIL 123
              VW       C   L G I      G C+A I+ ++ Q IFG YP  E WR  +  + 
Sbjct: 66  -NGVWDANSIRDCREILDGAI------GGCFAVIAERWPQLIFGNYPNEEYWRAVLAFVG 118

Query: 124 FILLLVPMLIPSAPRKGLNAILLF------------------------------------ 147
             + L P+L    PRK L    LF                                    
Sbjct: 119 LFVALAPVLFFKLPRKMLWFTGLFPFIAYWLIWGGSAWVSVMALVGVVVGYVAFKALEER 178

Query: 148 --------AVLPVIAFWLLHG-----------GFGLEVVETPLWGGLMVTLVLSFVGIAV 188
                   A+   + FW+                 L  VE+   GG M+  +L   GIA+
Sbjct: 179 SFFGAIVAALFATLLFWIFISPLAVNALSSVVALSLPQVESRFIGGFMINFILGTSGIAL 238

Query: 189 SLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLL 248
           SLP+GI LALGR+S +P+I+ +CV FIE IRGVPLIT+LF+ASVML  FLP G + D +L
Sbjct: 239 SLPLGIALALGRQSNLPIIKGVCVVFIEFIRGVPLITLLFVASVMLAYFLPPGTSFDLVL 298

Query: 249 RALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSI 308
           R +I +++F SAY+AE IRGGL A+P+GQ+E  DSLGL YWQ  RLII+PQA+K+ IPSI
Sbjct: 299 RVIIMITLFASAYIAEAIRGGLAALPRGQYEAGDSLGLDYWQSMRLIILPQALKISIPSI 358

Query: 309 VNTFIGTFKDTSLVTIIGMFDLLGIVK-LNFSDANWASAVTPITGLIFAGFIFWLFCFGM 367
           VN  IG FKDT+LV+II MFD+LG+++    S   W      + G  FAG +F++FC+G+
Sbjct: 359 VNIAIGLFKDTTLVSIISMFDMLGMIQGPILSSTEWFGVYWELLG--FAGVLFFVFCYGI 416

Query: 368 SRYSGFMERHLDTGHK 383
           S+YS ++ER L T H+
Sbjct: 417 SQYSQWLERQLATEHR 432


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: 40
Number of successful extensions: 7
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