GapMind for catabolism of small carbon sources

 

Alignments for a candidate for N515DRAFT_2924 in Methylocystis bryophila S285

Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease

Query= uniprot:A0A1I1Y8J0
         (492 letters)



>NCBI__GCF_002117405.1:WP_085770386.1
          Length = 488

 Score =  364 bits (934), Expect = e-105
 Identities = 205/488 (42%), Positives = 288/488 (59%), Gaps = 26/488 (5%)

Query: 2   LKNLFATTQISPASADLPGGGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAE 61
           L  LF    I    A+    GA     L+RAL    LV +G+G +IG GIFV+TG  AA 
Sbjct: 3   LVELFRAKSIESLQAEALERGA-----LRRALGLWQLVGIGLGGLIGVGIFVLTGVVAAT 57

Query: 62  HAGPAIVLSFVFAGIACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLE 121
            AGP + LSF+ AG+A   AALCYAEFA+MLPV+GSAY+Y+YA LGE  AW +GW L+LE
Sbjct: 58  QAGPGVALSFLIAGVASGAAALCYAEFASMLPVAGSAYTYAYAVLGELPAWIIGWDLLLE 117

Query: 122 YLFTVATVAAGWSGYFNKLLALISGWIGHDVSLPQTLAAAPFTVVDGHIQATGMFINLPA 181
           Y   VA V+ GWSGY   LLAL        V+ P+  A AP T  DGHI    +F  L A
Sbjct: 118 YALVVAVVSIGWSGYLRALLALFG------VAPPEWAAGAPGT-GDGHI--LDLFAMLGA 168

Query: 182 VAIIAAITGLCYVGITQSAFVNSIIVAIKVTVILLFIAFATKYINPDNWHPFIPASEGAS 241
             +   +T    + +   A  N+ +V +K+  +++ I  A  +INP NW PF+P      
Sbjct: 169 FGVALLLT----LRVEWGARFNTAMVLLKIAAVIVVILAAAPHINPANWRPFMP------ 218

Query: 242 KYGWAGVGRAAAIVFFSYIGFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGIL 301
            +G+ GV   AA+VFF+  G+D ++TA  EA  PQRD+P  ++ SL++   LYI+++  L
Sbjct: 219 -FGFGGVVEGAAVVFFAVFGYDTLTTAGEEALEPQRDLPRAVLLSLVVSLTLYILMSLAL 277

Query: 302 TGIADFRLLGTPEPVSTALDNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMAR 361
           TGIA +  L    PV++A      + W  ++V   AV G+ SVML  L+G  RI+++M+R
Sbjct: 278 TGIARYDTLDNAAPVASAFAAL-GMGWATLVVSAAAVVGILSVMLAFLLGCARIWFAMSR 336

Query: 362 DGLIPAVFGRIHQKFRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGV 421
           DGL+PA F R H +F TP+  T++ G L A +   F I  + E+V +GTL AF  +C+ V
Sbjct: 337 DGLLPAWFARPHPQFATPYRPTLIAGGLCALVSAFFPIREVAELVNIGTLSAFVVICLAV 396

Query: 422 LVLRYTRPELPRAFRVPVPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYG 481
           + LR+TRP++PR FR P+   +  +G    + L  +     W   + W+ IG A+YFLYG
Sbjct: 397 IALRHTRPDVPRGFRAPLSPYLPLIGVGFSLWLLSKLPAIAWERFVVWLIIGLAVYFLYG 456

Query: 482 YSHSKLRK 489
             HS+L K
Sbjct: 457 RRHSRLAK 464


Lambda     K      H
   0.328    0.141    0.441 

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: 715
Number of extensions: 45
Number of successful extensions: 5
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: 492
Length of database: 488
Length adjustment: 34
Effective length of query: 458
Effective length of database: 454
Effective search space:   207932
Effective search space used:   207932
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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