GapMind for catabolism of small carbon sources

 

Aligments for a candidate for N515DRAFT_2924 in Paraburkholderia bryophila 376MFSha3.1

Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate H281DRAFT_02180 H281DRAFT_02180 amino acid/polyamine/organocation transporter, APC superfamily

Query= uniprot:A0A1I1Y8J0
         (492 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02180 H281DRAFT_02180 amino
           acid/polyamine/organocation transporter, APC superfamily
          Length = 463

 Score =  402 bits (1033), Expect = e-116
 Identities = 219/464 (47%), Positives = 290/464 (62%), Gaps = 21/464 (4%)

Query: 27  ATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCYA 86
           A LK+AL A  L  LG+GAIIG GIFV+TG  A + AGPA+++SF+ A +AC  AAL YA
Sbjct: 20  AGLKKALGALDLTFLGVGAIIGTGIFVLTGTGAVQ-AGPALMVSFLIAAVACGFAALAYA 78

Query: 87  EFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALISG 146
           EFA+ +PV+GS Y+YSYATLGE  AW +GW L+LEY    + V+ GWSGY   LL+    
Sbjct: 79  EFASTIPVAGSIYTYSYATLGELAAWIIGWDLMLEYGLATSAVSVGWSGYLQSLLS---- 134

Query: 147 WIGHDVSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSII 206
             G  VSLP  L AAP     G +       NLPA  ++ AIT L  VG+ +SA +N+I+
Sbjct: 135 --GFGVSLPVALTAAP-----GALPGHETLFNLPAFLVMMAITALLSVGVRESARINNIM 187

Query: 207 VAIKVTVILLFIAFATKYINPDNWHPFIPASEGASKYGWAGVGRAAAIVFFSYIGFDAVS 266
           VAIKV V+LL IA    ++ P NWHPF+P        GW GV  AAA++FF++IGFD+VS
Sbjct: 188 VAIKVVVVLLVIAVGVFHVTPANWHPFMPN-------GWNGVFGAAAVMFFAFIGFDSVS 240

Query: 267 TAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIA-DFRLLGTPEPVSTALDNYPS 325
           +AA E KNP+RD+PIGII SL +C +LY+ VA ++TGI    +      PVS AL     
Sbjct: 241 SAAEEVKNPKRDLPIGIIASLGVCAVLYVAVAAVVTGIVPSAQFANISHPVSYALQ-VAG 299

Query: 326 LHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTVV 385
             W+   + +GAV G+ +V+LVM  GQ R+ ++M+RDGL+PA   R+H +F TP   T +
Sbjct: 300 QKWVAGFIDLGAVLGMLTVILVMAYGQTRVIFAMSRDGLLPARLSRVHPRFATPFFTTWL 359

Query: 386 VGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVPVPWIVCP 445
           VG+    +G L  + VL E++ +GTL AF+ V I VLVLR T PELPRAFR P   +V  
Sbjct: 360 VGIFFGLIGALVPLNVLAELINIGTLAAFSMVSIAVLVLRKTHPELPRAFRCPGVPVVPV 419

Query: 446 LGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKLRK 489
           L   +C+ L        W   + W+ IG  IYF Y    S L +
Sbjct: 420 LAVASCVFLMANLQAVTWVAFVVWLLIGMVIYFGYSRRRSHLAR 463


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: 722
Number of extensions: 43
Number of successful extensions: 7
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: 463
Length adjustment: 34
Effective length of query: 458
Effective length of database: 429
Effective search space:   196482
Effective search space used:   196482
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: 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 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, the preprint on GapMind for carbon sources, 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