Alignments for a candidate for Dshi_1194 in Desulfoscipio geothermicus DSM 3669

GapMind for catabolism of small carbon sources

Alignments for a candidate for Dshi_1194 in Desulfoscipio geothermicus DSM 3669

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_092487225.1 BM299_RS16955 TRAP transporter permease

Query= uniprot:E4PQE4
         (729 letters)



>NCBI__GCF_900115975.1:WP_092487225.1
          Length = 643

 Score =  434 bits (1117), Expect = e-126
 Identities = 229/543 (42%), Positives = 343/543 (63%), Gaps = 5/543 (0%)

Query: 171 SVPDLVLIVCSLAVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIMELTRRVAGM 230
           ++ D VL V  L+ + Y    Y T M    G +     + F AIA   L+ E+TRR  G 
Sbjct: 80  TITDFVLAVLLLSSSVYVAFNY-TEMLDRVGVAPTRWDLFFGAIALLGLL-EITRRTTGW 137

Query: 231 ALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQVYTDAGILGPTTAVSSTYIILFII 290
           AL ++G++FL Y + G   PG L + G S  R  S +++  GI      VS+ Y+ +FI+
Sbjct: 138 ALPVLGVIFLGYAYLGNIFPGDLWHKGYSWDRIISYMFSMDGIYNIPLGVSANYVFIFIL 197

Query: 291 FAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIP 350
           F +FL+ S  G +F++ A++ AGR RGGPAKVS+ +S +MG ++G++  NV STG+ TIP
Sbjct: 198 FGSFLEVSGCGKFFIDLAYSIAGRFRGGPAKVSVISSAMMGSVSGSAVANVASTGAFTIP 257

Query: 351 LMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYF 410
           LMK+VGY    AGAVEA ASTGGQI+PP+MGAGAFIMA+ITGI Y+ I IAAIIPA+LYF
Sbjct: 258 LMKRVGYKPAFAGAVEAVASTGGQILPPVMGAGAFIMADITGISYSTIIIAAIIPALLYF 317

Query: 411 ASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQ-CYLFVPIIILIVALF-MGYSVIRAGT 468
            +V FMVDFEA K G+ G+ + ELP  + ++K+   L +P+++++ +L  +  S +RA  
Sbjct: 318 LAVIFMVDFEAGKLGLMGLPKSELPNTKNILKERGILLIPLLVMLFSLLVLKNSPVRAAI 377

Query: 469 LATVSAAVVSWLSPNKMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFS 528
           L+  S  V+SW + NK+       ++  A      I    A AG+I+GV SLTG+GA+ +
Sbjct: 378 LSIGSLIVLSWFTKNKILFSQFFTSVSNAMKSMASIAATTACAGIIIGVFSLTGLGAKIA 437

Query: 529 VLLLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFV 588
             ++ ++  + ++AL+  M + +LLGMG+PT AAYA+AAS VAP LV +G+  L AH F+
Sbjct: 438 AFIIALSGGNLVIALVLVMLLCLLLGMGLPTVAAYALAASTVAPALVDMGVPLLAAHLFI 497

Query: 589 FYFAVVSAITPPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEAG 648
           FY+A +S ITPPV L+++A A I+GA  M     + ++GI +FI+PFMF  +  LL++  
Sbjct: 498 FYYACISTITPPVCLSAFAGAAIAGAPPMRVGWLAMKLGITSFIIPFMFMMDKTLLLQGE 557

Query: 649 WFEIARALVTATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIAL 708
              I   + TA  G+  LS G  G F     +W++R L + +A+L++   +W  + G+ L
Sbjct: 558 PVNIFIDVFTALIGIIALSAGAEG-FLVRKINWVSRTLFLVSAILLMAPKIWLSVPGLIL 616

Query: 709 AVL 711
            ++
Sbjct: 617 FLI 619


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: 1271
Number of extensions: 63
Number of successful extensions: 4
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: 643
Length adjustment: 39
Effective length of query: 690
Effective length of database: 604
Effective search space:   416760
Effective search space used:   416760
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: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources