GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Desulfovibrio vulgaris Miyazaki F

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 8502073 DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__Miya:8502073
          Length = 596

 Score =  140 bits (352), Expect = 1e-37
 Identities = 78/206 (37%), Positives = 122/206 (59%), Gaps = 6/206 (2%)

Query: 173 GGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASV 232
           GGL  +L+++ + I+VS  +G+ + +GR S   V R+ C+ +IE+IRG PLI V+F    
Sbjct: 388 GGLAYSLLMAVIAISVSFFIGLAVGVGRSSSNRVFRIPCLLYIELIRGNPLIIVIFWVYF 447

Query: 233 MLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKT 292
            +P+   T  NV     A   ++ FT AY+AE++R G+Q IP GQ E A S GL Y Q  
Sbjct: 448 FIPVMFGTTLNV--FWSATWALTAFTGAYIAEIVRTGIQNIPAGQVEAAYSTGLTYLQAM 505

Query: 293 RLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITG 352
           R I++PQA+K +IP+IV  FI  FKDTSL  ++G+ +L  + +      N    + P+  
Sbjct: 506 RRIVLPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLELTFVAQ----GINNRLMIHPMEI 561

Query: 353 LIFAGFIFWLFCFGMSRYSGFMERHL 378
                F++++ C+ MS ++  +ER L
Sbjct: 562 YGTVAFLYFICCYSMSVFAARLERRL 587



 Score =  105 bits (261), Expect = 4e-27
 Identities = 61/163 (37%), Positives = 94/163 (57%), Gaps = 6/163 (3%)

Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVM 233
           GL  T+ +S +  A++L +G +L L R S    +R+     IE  R  PL+  LF     
Sbjct: 60  GLANTVRISLISSALALLLGTMLGLARLSLFRPLRVTATCVIEFFRNTPLLIQLFFWYFA 119

Query: 234 LPLFLPTG-----WNVD-KLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLG 287
            P  LP       +++  +   A IG+SI+T+++MAEVIR GLQ+IPKG  E A S GL 
Sbjct: 120 FPAILPDNAREALFSIQFEFWCATIGLSIYTASFMAEVIRAGLQSIPKGLLEAAYSSGLS 179

Query: 288 YWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDL 330
           Y+Q  R II+P A + +IP + + F+   K++SL  ++G+ +L
Sbjct: 180 YFQVLRTIILPLAFRAIIPPLGSEFLNNMKNSSLAMVVGVAEL 222


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: 615
Number of extensions: 42
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 384
Length of database: 596
Length adjustment: 34
Effective length of query: 350
Effective length of database: 562
Effective search space:   196700
Effective search space used:   196700
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: 51 (24.3 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