GapMind for catabolism of small carbon sources

 

Aligments for a candidate for N515DRAFT_2924 in Pedobacter sp. GW460-11-11-14-LB5

Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate CA265_RS15145 CA265_RS15145 amino acid permease

Query= uniprot:A0A1I1Y8J0
         (492 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS15145 CA265_RS15145 amino acid
           permease
          Length = 649

 Score =  329 bits (844), Expect = 2e-94
 Identities = 189/475 (39%), Positives = 269/475 (56%), Gaps = 49/475 (10%)

Query: 1   MLKNLFATTQISPASADLPGGGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAA 60
           M + LF    IS    D   G    E TL + L  R L   GI AIIGAGIF   G+A+A
Sbjct: 1   MFEKLFRKKSISKILQDAAKGYGDHENTLHKTLGVRDLTAFGIAAIIGAGIFSTIGKASA 60

Query: 61  EHAGPAIVLSFVFAGIACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVL 120
           +  GPA++  F+F  +AC+ AA  YAEFA+M+PVSGSAY+YSY   GE VAW +GWSL++
Sbjct: 61  D-GGPAVIFLFIFTAVACSFAAFAYAEFASMVPVSGSAYTYSYVAFGELVAWIIGWSLIM 119

Query: 121 EYLFTVATVAAGWSGYFNKLLALIS----GWIGHDVSLPQTLAAAPFTVVDGHIQATGMF 176
           EY     TVA  WS YF  LL+ I     G  G  + +P  +     +  +GH  A  + 
Sbjct: 120 EYSIGNITVAISWSDYFTGLLSTIKIPPLGIEG--IHVPDWMTMDYLSAYNGHKHAEALL 177

Query: 177 I--------------------------------NLPAVAIIAAITGLCYVGITQSAFVNS 204
                                            ++PA+ II  IT L Y G+ +S   ++
Sbjct: 178 AAGKNLADLDSATALANNAWLTAPKIGSFHLVADIPALGIIILITWLIYRGMKESRNASN 237

Query: 205 IIVAIKVTVILLFIAFATKYINPDNWHPFIPASEGASKYGWAGVGRAAAIVFFSYIGFDA 264
            +V +K+ VILL +A    Y++  NW PF P        G +GV +  + VFF+YIGFDA
Sbjct: 238 AMVVVKLAVILLVLAVGIFYVDTKNWDPFAPN-------GVSGVLKGVSAVFFAYIGFDA 290

Query: 265 VSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPEPVSTALDNYP 324
           +ST A E KNPQRD+P G++ ++I+CTILY+ +A +LTGI     L   +P++   D   
Sbjct: 291 ISTTAEECKNPQRDLPRGMMWAIIICTILYVAIALVLTGIVKSDTLAVGDPLAFVFDQI- 349

Query: 325 SLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTV 384
           +L  +  I+ + AV  ++SV+LV  MGQPRI+ SM+RDGL+P  F +IH K++TP   T+
Sbjct: 350 NLKLMSGIIAVSAVFAMASVLLVFQMGQPRIWMSMSRDGLLPKSFSKIHPKYKTPSFATI 409

Query: 385 VVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRA-FRVP 438
           VVG + A      N+ ++ ++ ++GTL AF  VC GVLVL+  RP++ R  F++P
Sbjct: 410 VVGFVVAVPSLFMNLTIVTDLCSIGTLFAFVLVCAGVLVLQ-NRPDVQRGKFKIP 463



 Score = 43.9 bits (102), Expect = 2e-08
 Identities = 16/44 (36%), Positives = 26/44 (59%)

Query: 446 LGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKLRK 489
           LG ++C+ +  +  + +W     W+ +G  +YF YGY HSKL K
Sbjct: 603 LGLISCLYMMCELGISNWIGFGIWLVVGLVVYFAYGYRHSKLAK 646


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: 897
Number of extensions: 45
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 492
Length of database: 649
Length adjustment: 36
Effective length of query: 456
Effective length of database: 613
Effective search space:   279528
Effective search space used:   279528
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: 53 (25.0 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