GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_1194 in Nocardiopsis lucentensis DSM 44048

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_017597109.1 D471_RS0102170 TRAP transporter fused permease subunit

Query= uniprot:E4PQE4
         (729 letters)



>NCBI__GCF_000341125.1:WP_017597109.1
          Length = 724

 Score =  368 bits (944), Expect = e-106
 Identities = 240/699 (34%), Positives = 377/699 (53%), Gaps = 46/699 (6%)

Query: 10  LPDIEV--GEDHVLAHNVDEEPVEANRRLFEGGLLKFVALLAIAYSAFHLYSLNIAPLET 67
           LPD++   G D  L   V EE     R     G +  VA+LA+A +AF LY    A L+ 
Sbjct: 38  LPDVDGRDGGDGPLWRRVAEERWGEGRAATAVGAV--VAVLAVALTAFQLYVALFAGLDA 95

Query: 68  WSFRIVHIAGALVLGFVLFAGARFVSSEEGGARHRWTTWISAGAMLPALYVLYQTFSFWQ 127
              RI+H+   +VL F+L     F   +  G        +SA  ++ AL    +  +  +
Sbjct: 96  RQQRIIHLLFVMVLVFLLMRP--FDLGKASG--------LSALTVVRALIPRRRKGTV-K 144

Query: 128 MVQNGAMRIPVELEVWHFGWPLLAATGVGIVMSWFHQRERSVFSVPDLVLIVCSLAVAAY 187
               G  R      V          TGVG V+              DLVL+  ++ V+ Y
Sbjct: 145 GEDGGDPRDAAARRV---------LTGVGWVL--------------DLVLVTAAVVVSVY 181

Query: 188 FLVVYNTSMRMSTGTSFAPVGISFA-AIAGTALIMELTRRVAGMALVIIGLVFLAYVFAG 246
             + Y   +    G   A  G+ +   +    +++E TRR  GM +V++ + F+ Y + G
Sbjct: 182 -PIRYQDELAARAG---AYTGLDWVLGLILMIVLLEATRRAVGMIMVLLVVAFVYYAWIG 237

Query: 247 PYLPGFLGYPGLSVQRFFSQVYTDAGILGPTTAVSSTYIILFIIFAAFLQSSKVGDYFVN 306
           P++PG  G+ G ++QR  +  Y   GI G T  V  T++ +FI+F A L  +  G++FV 
Sbjct: 238 PFIPGQFGHTGATIQRISTHTYLGDGIYGLTLGVVVTFVFVFILFGALLNKTGGGNFFVG 297

Query: 307 FAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQSAGAVE 366
            A+   GR  GGPAK ++  S +MG ++G++  NVV++G  TIPLM+KVGY +  A  VE
Sbjct: 298 LAYVVTGRMVGGPAKGAVLGSAMMGSVSGSAIANVVTSGPFTIPLMRKVGYRRADAAGVE 357

Query: 367 AAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFASVYFMVDFEAAKTGM 426
           AAASTGGQI+PPIMGAGAFIMAE TGIPY +I   A+IPA++YF  ++  VD  A K G+
Sbjct: 358 AAASTGGQILPPIMGAGAFIMAERTGIPYADIVKVALIPALMYFGVMFLFVDILARKHGI 417

Query: 427 RGMREDELPKLRTMMKQCYLF-VPIIILIVALFMGYSVIRAGTLATVSAAVVSWL-SPNK 484
              R ++LP+LR +M   + F +P+++LIV L       +AG  A  +   V+ L + ++
Sbjct: 418 GVARNEDLPRLRLVMAAGWHFLLPLLLLIVLLLQYVPPTQAGLYACGALLAVAMLRAGSR 477

Query: 485 MGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQLLALI 544
           +    +L    +A+   + +   CA AG+IVG++ LTG+G   S +L+ V A + LL L+
Sbjct: 478 LSPSDLLDVFVMAARNTLPVSAACAVAGIIVGMVGLTGLGLTLSNVLVTVFAGNLLLTLV 537

Query: 545 FAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPPVALA 604
                S+++G G+P TA+Y V + +  P L +LG+  L AH  V++++  S +TPPVALA
Sbjct: 538 MVAVASLIMGFGLPVTASYVVISVLAVPALGELGLTVLVAHMIVYWYSQDSNVTPPVALA 597

Query: 605 SYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEAGWFEIARALVTATFGVY 664
           ++AAAGI+GA  M    A+++     +++P M  Y+  L ++    E+A A+++    + 
Sbjct: 598 AFAAAGIAGAKPMRAGAAAWKFAKGLYLIPVMMAYSALLAVDGPVLELAAAVLSGCVALA 657

Query: 665 MLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDL 703
             +  + G F   +       L++AAAL+M+ G  W  L
Sbjct: 658 AAAIAIEGHFLRRTTLGERLGLILAAALVMV-GPEWAAL 695


Lambda     K      H
   0.327    0.139    0.410 

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: 1293
Number of extensions: 60
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 729
Length of database: 724
Length adjustment: 40
Effective length of query: 689
Effective length of database: 684
Effective search space:   471276
Effective search space used:   471276
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: 55 (25.8 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