GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PGA1_c12650 in Pseudomonas stutzeri RCH2

Align D-lactate transporter, permease component 1 (characterized)
to candidate GFF3787 Psest_3856 ABC-type branched-chain amino acid transport system, permease component

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



>lcl|FitnessBrowser__psRCH2:GFF3787 Psest_3856 ABC-type
           branched-chain amino acid transport system, permease
           component
          Length = 328

 Score =  169 bits (427), Expect = 1e-46
 Identities = 106/312 (33%), Positives = 157/312 (50%), Gaps = 48/312 (15%)

Query: 9   KTLLLVVAILTL-FAPFILNPFPTGSALAQFNAGYPDLMQRFVIFGIFAIGFNILFGLTG 67
           +T+L+++ ++ L  APF                 YP  + + + F +FA  FN+L G TG
Sbjct: 19  ETVLILIGVIALALAPFYF---------------YPIFLMKVLCFALFACAFNLLLGYTG 63

Query: 68  YLSFGHAAFLGVGSYSAVWMFKLLSMNVVPAIVLSVIVAGLFALVIGYVSLRRSGIYFSI 127
            LSFGHAAF G  +Y      K   +     I++ V  A    L+IG++++RR GIY ++
Sbjct: 64  ILSFGHAAFFGGAAYFTAHAVKEWGLTPELGILVGVAGAAFLGLIIGFLAIRRQGIYSTM 123

Query: 128 LTLAFAQMSFNLAYSVLTPITNGETGLQLTLDDPRVLGVSATADGSIPVTSLFGL-EMRS 186
           +TLA +QM F   + +    T+GE G+Q                 +IP   LFGL ++  
Sbjct: 124 ITLALSQMFF--FFCLQASFTHGEDGIQ-----------------NIPRGHLFGLIDLEE 164

Query: 187 TFEMVVGPWAFQFNAGYYLCALILLAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNT 246
              M            Y+    + LA   L  R+  SP+G++L++++ N+ R    G + 
Sbjct: 165 PLYM------------YFFVLSVFLAGMLLIWRVIHSPYGMILRSIRENENRAISLGYSV 212

Query: 247 RPYTLAAFVISGMYAGLAGGLMASMDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVLG 306
             Y L AFV+S   AGLAGGL A +   A    + W  SGEVVLMT+LGG GTL+GPV G
Sbjct: 213 SRYKLGAFVMSAALAGLAGGLKALVFQFATLTDVSWQMSGEVVLMTLLGGIGTLVGPVFG 272

Query: 307 AGFIKYFENIFS 318
           A  +    N F+
Sbjct: 273 AALVTTLGNYFA 284


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: 414
Number of extensions: 29
Number of successful extensions: 2
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: 328
Length adjustment: 29
Effective length of query: 371
Effective length of database: 299
Effective search space:   110929
Effective search space used:   110929
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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