Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_007154429.1 MDG893_RS13850 TRAP transporter permease
Query= uniprot:E4PQE4 (729 letters) >NCBI__GCF_000170835.1:WP_007154429.1 Length = 726 Score = 1275 bits (3299), Expect = 0.0 Identities = 654/725 (90%), Positives = 691/725 (95%) Query: 1 MTTEQDSKDLPDIEVGEDHVLAHNVDEEPVEANRRLFEGGLLKFVALLAIAYSAFHLYSL 60 MT +Q ++ P ++G+DHVLAH+VDEEPVEANRRLF+GG+LKFV LLAIAYS+FHLYSL Sbjct: 1 MTDKQHPEEHPVNDIGDDHVLAHDVDEEPVEANRRLFKGGMLKFVTLLAIAYSSFHLYSL 60 Query: 61 NIAPLETWSFRIVHIAGALVLGFVLFAGARFVSSEEGGARHRWTTWISAGAMLPALYVLY 120 NIAPLETWSFRIVHIAGALVLGF+LFAGARFVS+EEG ARHRWTTWI A AM+PA+Y LY Sbjct: 61 NIAPLETWSFRIVHIAGALVLGFILFAGARFVSAEEGPARHRWTTWIGALAMVPAVYALY 120 Query: 121 QTFSFWQMVQNGAMRIPVELEVWHFGWPLLAATGVGIVMSWFHQRERSVFSVPDLVLIVC 180 QTFSF QM+ G +RIPV+LE WHFGWPLLAA+ +GIVMSWFHQRERS FSVPDLVLIVC Sbjct: 121 QTFSFHQMILGGTLRIPVDLETWHFGWPLLAASAIGIVMSWFHQRERSRFSVPDLVLIVC 180 Query: 181 SLAVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIMELTRRVAGMALVIIGLVFL 240 S+AVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIMELTRRVAG+ALV+IGLVFL Sbjct: 181 SVAVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIMELTRRVAGLALVVIGLVFL 240 Query: 241 AYVFAGPYLPGFLGYPGLSVQRFFSQVYTDAGILGPTTAVSSTYIILFIIFAAFLQSSKV 300 YVF GPYLPGFLGYPGLSVQRFFSQVYTDAGILGPTTAVSSTYIILFI+FAAFLQ+SKV Sbjct: 241 VYVFLGPYLPGFLGYPGLSVQRFFSQVYTDAGILGPTTAVSSTYIILFIVFAAFLQASKV 300 Query: 301 GDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQ 360 GDYFVNFAFAAAGR+RGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQ Sbjct: 301 GDYFVNFAFAAAGRTRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQ 360 Query: 361 SAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFASVYFMVDFE 420 SAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFASVYFMVDFE Sbjct: 361 SAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFASVYFMVDFE 420 Query: 421 AAKTGMRGMREDELPKLRTMMKQCYLFVPIIILIVALFMGYSVIRAGTLATVSAAVVSWL 480 AAKTGMRGMREDELPKL+TM+KQCYLFVPIIILIVALFMGYSVIRAGTLATVSAAVVSW Sbjct: 421 AAKTGMRGMREDELPKLKTMVKQCYLFVPIIILIVALFMGYSVIRAGTLATVSAAVVSWF 480 Query: 481 SPNKMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQL 540 SPNKMG+R IL+ALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVA SQL Sbjct: 481 SPNKMGIRKILEALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAEASQL 540 Query: 541 LALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPP 600 LALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPP Sbjct: 541 LALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPP 600 Query: 601 VALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEAGWFEIARALVTAT 660 VALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLM+AGWF+IARAL+TA Sbjct: 601 VALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMDAGWFDIARALITAL 660 Query: 661 FGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAFVIQKQRK 720 FGVYMLSGGVLGWFA SA ITRLLLI AALLMIEGGLWTDL+GIALAV+AF+ Q+Q K Sbjct: 661 FGVYMLSGGVLGWFARASAGVITRLLLIGAALLMIEGGLWTDLSGIALAVIAFLAQRQSK 720 Query: 721 TRLAT 725 R A+ Sbjct: 721 LRPAS 725 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: 1755 Number of extensions: 72 Number of successful extensions: 1 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: 729 Length of database: 726 Length adjustment: 40 Effective length of query: 689 Effective length of database: 686 Effective search space: 472654 Effective search space used: 472654 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
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