GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ga0059261_1577 in Pedobacter sp. GW460-11-11-14-LB5

Align L-glutamine and L-histidine transporter (characterized)
to candidate CA265_RS15000 CA265_RS15000 amino acid permease

Query= reanno::Korea:Ga0059261_1577
         (470 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS15000 CA265_RS15000 amino acid
           permease
          Length = 491

 Score =  305 bits (780), Expect = 3e-87
 Identities = 174/491 (35%), Positives = 267/491 (54%), Gaps = 25/491 (5%)

Query: 4   GLFRTKRVKDAAEQAPEHR--LAATLSWPHLVALGVGAIVGTGILTLIGVGAGK-AGPAV 60
           GLF  K +    E+A +    L  TLS   LVALGVGAI+G G+       A + AGP+V
Sbjct: 2   GLFTKKPMHLLLEEAGDSGKGLKRTLSAGALVALGVGAIIGAGLFVRTAAAAAQNAGPSV 61

Query: 61  IMSFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVS 120
            + F+IA   CA A L YAE+++ +P SGSAY Y+YA +GE++AWV+GW L+LEY++  +
Sbjct: 62  TIGFIIAAIGCALAGLCYAELSSSIPISGSAYTYTYATMGELMAWVIGWDLVLEYAVGAA 121

Query: 121 TVAVGWSGY----------AAPLLHAWTGMPLELMAGPHANGIVNLPAIFIIAVVAGLLC 170
           TV + WS Y           +P+ + W   P +       NGI+NLPA+FI+ +++ LL 
Sbjct: 122 TVGIAWSEYLNKLLVEVLHTSPIPYEWCHSPFQSHPDGTVNGIMNLPALFIVGLLSLLLI 181

Query: 171 LGTKESATLNAALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVER---- 226
            GT ESA +N  +V+ K+  + + + +   + N +N  P+ P      +   G+      
Sbjct: 182 KGTSESAFVNGLIVITKVGIVILIIVLGWGFINESNHHPYIP-AATTYVDHAGISHSFGG 240

Query: 227 --GVMAAAAIIFFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGA 284
             GV+ AA  +FFAF GFDA+STAA+ETKNP   + IGI+GS+  C  +Y+L A    G 
Sbjct: 241 FWGVIGAAGTVFFAFIGFDAVSTAAQETKNPKTAMPIGILGSLAVCTVLYILFAHVLTGI 300

Query: 285 TPFTHFANSPEPLALILR----DLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMA 340
            P   F       +++        G    +  + V+ +    +V+L  L GQSR+F++M+
Sbjct: 301 APVEFFRTKGGEASVVAAISEYMTGYSWLSKLVTVAILAGFSSVILVMLLGQSRVFYSMS 360

Query: 341 RDGMLPIGLAKV-SKRGSPVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVC 399
           +DG+LP   + +  K  +P +  L    IV + A  +P D +  + + GTL AF  V V 
Sbjct: 361 KDGLLPKMFSDLHPKFKTPYKANLVILIIVGLFAAFIPGDVVGDMTSIGTLFAFMLVCVA 420

Query: 400 MMVLRVRAPDMPRMFRTPLWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAY 459
           +++LR   PD+PR F+TP   L+  + V+ C  +   L     L    W ALG +IYF Y
Sbjct: 421 VIILRKTDPDLPRQFKTPWVPLIPILGVVACGLMILGLGWTNWLRLFGWLALGFIIYFGY 480

Query: 460 ARPRVSAKGIE 470
           ++     K ++
Sbjct: 481 SKKNSHLKDVK 491


Lambda     K      H
   0.327    0.140    0.426 

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: 686
Number of extensions: 44
Number of successful extensions: 9
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: 470
Length of database: 491
Length adjustment: 34
Effective length of query: 436
Effective length of database: 457
Effective search space:   199252
Effective search space used:   199252
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