GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12650 in Dinoroseobacter shibae DFL-12

Align D-lactate transporter, permease component 1 (characterized)
to candidate 3607447 Dshi_0860 inner-membrane translocator (RefSeq)

Query= reanno::Phaeo:GFF1249
         (400 letters)



>FitnessBrowser__Dino:3607447
          Length = 324

 Score =  130 bits (327), Expect = 5e-35
 Identities = 104/351 (29%), Positives = 148/351 (42%), Gaps = 76/351 (21%)

Query: 45  LMQRFVIFGIFAIGFNILFGLTGYLSFGHAAFLGVGSYSAVWM--------------FKL 90
           L  R  I  +  +G N+  GL G +S GHA F G+G Y+   +              F +
Sbjct: 33  LATRVAILALAGVGLNLALGLGGMVSLGHALFFGIGGYAMGILAHHAQTFDPLMEAPFVI 92

Query: 91  LSMNVVPAIVLSVI-VAGLFALVIGYVSLRRSGIYFSILTLAFAQMSFNLAYSVLTPITN 149
                +P I L+ + ++ L AL +G +SLR +G+YF ++TLAF QM +  A S   P   
Sbjct: 93  EGTKSMPVIWLTAMALSALAALAVGALSLRTTGVYFIMITLAFGQMFYYFAIS--WPAYG 150

Query: 150 GETGLQLTLDDPRVLGVSATADGSIPVTSLFGLEMRSTFEMVVGPWAFQFNAGYYLCALI 209
           GE GL + + +                    G    +T + +      QF   + LC  +
Sbjct: 151 GEDGLSIYVRN--------------------GFPGLNTLDPI------QF---FLLCYGL 181

Query: 210 LLAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNTRPYTLAAFVISGMYAGLAGGLMA 269
           LL A ++  RI  SPFGL L   +    R    G +     L AF ISG   GLAG L A
Sbjct: 182 LLLALFVCARITASPFGLALSTARQAPARAETLGFSPFRLRLIAFTISGAITGLAGALFA 241

Query: 270 SMDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVLGAGFIKYFENIFSKINDNVLHSWF 329
            ++         W  SGE+++  ILGG   L GPV GA      E+    +++       
Sbjct: 242 DLNRFVSPAMFSWHTSGEIMVFVILGGVARLFGPVAGAALFILLEHWLGGLSEY------ 295

Query: 330 SFMPDGIEDAMVFIVHPFIGKGWHLTLGILFMLVVIFLPGGLVEGGQKLRG 380
                                 W + LG L + VV+F  GGLV  G  LRG
Sbjct: 296 ----------------------WLIYLGALLLGVVLFAKGGLV--GTLLRG 322


Lambda     K      H
   0.327    0.143    0.435 

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: 420
Number of extensions: 32
Number of successful extensions: 4
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: 400
Length of database: 324
Length adjustment: 29
Effective length of query: 371
Effective length of database: 295
Effective search space:   109445
Effective search space used:   109445
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: 49 (23.5 bits)

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

Links

Downloads

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:

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