GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Psest_0084 in Marinobacter algicola DG893

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.

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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