GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF3787
          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.

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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