GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CCNA_00435 in Lysobacter daejeonensis GH1-9

Align Amino acid transporter (characterized, see rationale)
to candidate WP_036136365.1 N800_RS06840 amino acid permease

Query= uniprot:A0A0H3C3Q5
         (483 letters)



>NCBI__GCF_000768355.1:WP_036136365.1
          Length = 474

 Score =  293 bits (750), Expect = 9e-84
 Identities = 171/467 (36%), Positives = 267/467 (57%), Gaps = 18/467 (3%)

Query: 22  AGHADSH--QLKKTLSWPHLVALGVGAIVGTGIYTLTG-VGAGLAGPGVILSFLIAGAVC 78
           A HAD+    L +TL    L ALG+GA++G GI+ +TG   A  AGP ++LSF++A   C
Sbjct: 13  AAHADADGLSLHRTLGKWGLTALGIGAVIGGGIFVITGQAAADHAGPAIMLSFVLAAICC 72

Query: 79  ACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVGWSAHAH 138
              AL YAE ++M+P SGSAYTY+YA +GE  AWF+GW L+LEY +  +AVAV W+ +  
Sbjct: 73  TFCALAYAEFASMVPVSGSAYTYTYATLGELAAWFIGWMLVLEYGVSASAVAVSWTGYFL 132

Query: 139 GLFKM--IGFPDALLAGPHQ------GGLINMPAVFISMAVAGLLALGTRESATVNMVLV 190
            L +   I  P AL+  P        G + N+PA  I + +  +  +G R+S+ +N  +V
Sbjct: 133 SLLEHFNIHLPAALVQAPLDSKLQPTGAIANLPAAAIVLLLTWVCYIGIRKSSGMNTAMV 192

Query: 191 FVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFFAFY 250
            +K   +++ ++      + A++ PF+P        EG      + GV+  AS++FFA+ 
Sbjct: 193 LLKSGLIVLVIIAGWQYVDPANWEPFIPAN------EGPGKFGWE-GVLRGASMVFFAYI 245

Query: 251 GFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPLVFI 310
           GF+AVS AA+E+ NP++DL  G++ S+A+CT +Y+ +AAV  G +   +    E  +  +
Sbjct: 246 GFEAVSVAAQESHNPQKDLPFGMLMSLAICTVLYIGMAAVMTGLTPYTLLGTDEPVVTAV 305

Query: 311 LESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGTPV 370
                   +  +V + A+I L +V+L  + GQ RIF +MARDGLLP   ++++ K  TP 
Sbjct: 306 AGHAELAWLRVVVEIGALIGLSSVVLVMIIGQPRIFMIMARDGLLPEVFTRIHPKHRTPH 365

Query: 371 MMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFSTPLW 430
           + T++TG+  A+++ +  L  + EL + GTL AF AV A V++LR  +P+ PR F     
Sbjct: 366 INTVITGIGIALLAAVFPLDILGELTSMGTLIAFGAVCAGVLILRRTQPDLPRPFRIRGV 425

Query: 431 PIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVL 477
             V  AGI  CL L  ++     +  L    +G  +Y  YG R S L
Sbjct: 426 WFVCLAGIFSCLALLSAMTLHNWMLMLGWTTVGFAIYFLYGYRHSKL 472


Lambda     K      H
   0.326    0.138    0.415 

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: 674
Number of extensions: 40
Number of successful extensions: 4
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: 483
Length of database: 474
Length adjustment: 34
Effective length of query: 449
Effective length of database: 440
Effective search space:   197560
Effective search space used:   197560
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 24 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