GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3606890 Dshi_0320 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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