Alignments for a candidate for Psest_0084 in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Dinoroseobacter shibae DFL-12

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate 3607679 Dshi_1088 TRAP transporter, 4TM/12TM fusion protein (RefSeq)

Query= uniprot:E4PQE4
         (729 letters)



>FitnessBrowser__Dino:3607679
          Length = 595

 Score =  321 bits (823), Expect = 6e-92
 Identities = 190/533 (35%), Positives = 300/533 (56%), Gaps = 16/533 (3%)

Query: 178 IVCSLAVAAYFLVVYNTSMRMSTGTSFAPVGISFA-AIAGTALIMELTRRVAGMALVIIG 236
           I+  L +A    +  N  M +     F   G   A AI    + ME  RR  G  L ++ 
Sbjct: 68  ILTGLGIAGCLWIALNHQM-LRNQYGFLESGFQVALAITLLLVAMEGARRAIGWPLPLVA 126

Query: 237 LVFLAYVFAGPYLPGFLGYPGLSVQRFFSQ-VYTDAGILGPTTAVSSTYIILFIIFAAFL 295
           L+ L Y   G ++PG  G+ G  ++ F    V  + G+ G  T VS   + +F+IF A L
Sbjct: 127 LLALLYGLYGQHIPGEFGHAGTPLRSFLGTLVVAEGGLWGSLTGVSVGVVAVFVIFGAVL 186

Query: 296 QSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLMKKV 355
            + + G  F+N A AAAGR +GG AKVS+ +S L G I+G+++ NV STG++T+P M K+
Sbjct: 187 NAGEAGQGFMNVAAAAAGRLKGGAAKVSVLSSALFGSISGSASANVASTGAITLPAMTKL 246

Query: 356 GYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFASVYF 415
           GY ++ A A EA AS+GGQIMPP+MGAGAF+M E+TG+PY+EI +AA++PAILYFA+V+ 
Sbjct: 247 GYPRRLAAATEAVASSGGQIMPPLMGAGAFVMVELTGVPYSEIMLAALLPAILYFATVWQ 306

Query: 416 MVDFEAAKTGMRGMREDELPKLR-TMMKQCYLFVPIIILIVALF-MGYSVIRAGTLATVS 473
            ++  A++  +R +  ++ P  R  ++   +  VP   L++A+F +GY+   A  LA  +
Sbjct: 307 GLNAFASRYDLRPIPVEDRPARRQVLITSGFFLVPFSTLLIAMFALGYTPQYAAALAIFT 366

Query: 474 AAVVSW----LSPNK-MGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFS 528
              + +    L PN   G   + +AL  A      I  +   A +I+GV+ +TG+G + +
Sbjct: 367 GLALLFVDISLRPNPGQGFARLAEALLNAGKQVSMIAAIIICASIIIGVLGITGLGVKIT 426

Query: 529 VLLLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFV 588
            ++L  +  +   AL+      +LLGM +PTTAAY +  SV  P L++LG+EPL AH FV
Sbjct: 427 SVILSGSGGALWPALLLTALACLLLGMEVPTTAAYVICVSVAGPALIELGLEPLQAHLFV 486

Query: 589 FYFAVVSAITPPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALL-MEA 647
           F+FA++S ITPPV  A + A+G+   N +  ++ +  +G+  +++P     N AL+ + A
Sbjct: 487 FWFALLSTITPPVCGAVFIASGMVQENWLRVALTAMALGVGLYVIPLAMIANDALIRLSA 546

Query: 648 GWFEIARALVTATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLW 700
                  AL+    G+  +S G++G        W  R+ + A  L +    LW
Sbjct: 547 EPGAALLALLVVGAGLGGVSRGLIG-----REPWPLRVAVCAGGLGLCFAALW 594



 Score = 31.6 bits (70), Expect = 1e-04
 Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 7/69 (10%)

Query: 648 GWFEIARALVTATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIA 707
           GW     AL+   +G+Y     + G F        T L      L++ EGGLW  LTG++
Sbjct: 119 GWPLPLVALLALLYGLY--GQHIPGEFGHAG----TPLRSFLGTLVVAEGGLWGSLTGVS 172

Query: 708 LAVLA-FVI 715
           + V+A FVI
Sbjct: 173 VGVVAVFVI 181


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: 1100
Number of extensions: 63
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: 595
Length adjustment: 38
Effective length of query: 691
Effective length of database: 557
Effective search space:   384887
Effective search space used:   384887
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 Sep 17 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:

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 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