GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Psest_0084 in Pseudomonas litoralis 2SM5

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_090272364.1 BLU11_RS05175 TRAP transporter permease

Query= uniprot:E4PQE4
         (729 letters)



>NCBI__GCF_900105005.1:WP_090272364.1
          Length = 862

 Score =  218 bits (555), Expect = 1e-60
 Identities = 128/373 (34%), Positives = 204/373 (54%), Gaps = 35/373 (9%)

Query: 162 FHQRERSVFSVPDLVLIVCSLAVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIM 221
           F +  R+   + D V+ +     AAY  + Y          +   V +   A+ G  L++
Sbjct: 87  FRRSPRNHVPLTDWVMALVGAFCAAYIYIFYAALAERPGSPTTTDVVV---ALVGLVLLL 143

Query: 222 ELTRRVAGMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFS-QVYTDAGILGPTTAV 280
           E TRR  G  L+I+ L+F+ Y  AGPY+PG L + G+S+    + Q  +  G+ G    V
Sbjct: 144 EATRRALGPPLMIVALLFIIYSVAGPYMPGMLAHRGVSLTSLANHQWLSTQGVFGIALGV 203

Query: 281 SSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGN 340
           S++++ LF++F + L  +  G+YF+  AF+  G  RGGPAK ++ ASG+ G+I+G+S  N
Sbjct: 204 STSFVFLFVLFGSLLDKAGAGNYFIKLAFSLLGHYRGGPAKAAVAASGMTGLISGSSIAN 263

Query: 341 VVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAI 400
            V+TG+ TIP+MK+VGY+ + AGAVE +AS  GQIMPP+MGA AF+M E  GI YTE+  
Sbjct: 264 TVTTGTFTIPMMKRVGYTAEQAGAVEVSASVNGQIMPPVMGAAAFLMVEYVGISYTEVIT 323

Query: 401 AAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQCYLFVPIIILIVALFMG 460
            A +PA++ + +++++V   A K GM+G+       +R   ++   F+  ++LI+ L   
Sbjct: 324 HAFLPAMISYIALFYIVHLAALKAGMQGLESSN--PVRPFARKMLGFLTGLLLIMGL--- 378

Query: 461 YSVIRAGTLATVSAAVVSWLSPNKMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISL 520
                  +LA      + WL P          AL + +   I       AAG+ +  I+L
Sbjct: 379 -------SLAVYYG--LGWLKP----------ALGVYASWVI-------AAGLAIAYIAL 412

Query: 521 TGVGARFSVLLLD 533
             VG+ +  L LD
Sbjct: 413 LRVGSHYPDLDLD 425



 Score =  132 bits (333), Expect = 6e-35
 Identities = 104/330 (31%), Positives = 162/330 (49%), Gaps = 32/330 (9%)

Query: 398 IAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLR-TMMKQCYLFVPIIILIVA 456
           +AIA I  A+L   S Y  +D +   + +  M     P+ R T+M   +  +P+I+L+  
Sbjct: 405 LAIAYI--ALLRVGSHYPDLDLDDPNSPVVSM-----PQTRPTLMTGLHFILPVIVLVWC 457

Query: 457 LFMG-YSVIRAGTLATVSAAVVSW--------------LSPN-KMGLRHILQALEIASYM 500
           L +   S   +   ATV   ++                L  N + G     + L   +  
Sbjct: 458 LMVERLSPALSAFWATVFMTIIMLTQHPLIAMFRKERDLGRNIRRGFCDFWEGLVAGARN 517

Query: 501 AIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQLLALIFAMFISILLGMGMPTT 560
            I I +  A AG+IVG +S TGVG   + L+  ++  + LL L     +S++LGMG+PTT
Sbjct: 518 MIGIGIATATAGIIVGAVSQTGVGLVLADLVEVLSMGNLLLMLALTAVLSLILGMGLPTT 577

Query: 561 AAYAVAASVVAPGLVQLG-----IEPLTA-HFFVFYFAVVSAITPPVALASYAAAGISGA 614
           A Y V ++++AP +V LG     I PL A H FVFYF +++ +TPPV LAS+AAA ISG 
Sbjct: 578 ANYIVVSALLAPVIVTLGQQNGLIVPLIAVHLFVFYFGIMADVTPPVGLASFAAAAISGG 637

Query: 615 NAMETSVASFRIGIAAFIVPFMFFYNGALLMEAGWFEIARAL-VTATFGVYMLSGGVLGW 673
           + + T   +F   +    +PF+F +N  LL+    F     + V AT  + + +    GW
Sbjct: 638 DPIRTGFQAFYYSLRTAALPFLFIFNTDLLLIDVSFTYGLVIFVVATVAMLIFAAATQGW 697

Query: 674 FASISASWITRLLLIAAALLMIEGGLWTDL 703
             + S  W    LL+  A  +   G W D+
Sbjct: 698 MITRS-RWYESALLLLVAFTLFRPGFWMDM 726


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: 1524
Number of extensions: 90
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 729
Length of database: 862
Length adjustment: 41
Effective length of query: 688
Effective length of database: 821
Effective search space:   564848
Effective search space used:   564848
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