GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuK in Pseudomonas stutzeri RCH2

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate GFF3990 Psest_4063 sulfate ABC transporter, ATP-binding protein

Query= TCDB::Q9R9Q4
         (342 letters)



>lcl|FitnessBrowser__psRCH2:GFF3990 Psest_4063 sulfate ABC
           transporter, ATP-binding protein
          Length = 334

 Score =  213 bits (543), Expect = 4e-60
 Identities = 126/332 (37%), Positives = 191/332 (57%), Gaps = 16/332 (4%)

Query: 4   LQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFD 63
           +++  I K FG F  +  +++ I+ GE +  +GPSGCGK++LLR+IAGLE   SG++ F 
Sbjct: 3   IEISHINKRFGQFQALNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSIVFH 62

Query: 64  GQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCR----KRVEAAAE 119
           G+ V+      R +  VFQ YAL+ HMTV+EN+AFG+++  K ++       ++V     
Sbjct: 63  GEDVSSRDVRDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEKVHELLG 122

Query: 120 MLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKL 179
           ++QL    +R P QLSGGQRQR+A+ RA+  +PKV L DEP   LDA +R   R  +A+L
Sbjct: 123 LVQLDWLADRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLARL 182

Query: 180 HRSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPK 239
           H  +H T+ ++VTHDQ EAM +ADRI V+  G++EQIGTP E+Y  P S FV  F+G   
Sbjct: 183 HEDVHLTS-VFVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEVYANPASEFVYDFLGDAN 241

Query: 240 MNFLSGAFAEPYKADTIGIR----AEHL--EIDEQGGEWSGTVIHSEMLGSDSYIYLDIG 293
              L    +  ++   + +     AEHL  E+ +     + T +  ++ G    I  ++G
Sbjct: 242 RLQLDDQRSVLFRPHEVALSREAVAEHLAGEVRDIRPLGALTRVTLKVAGQAEPIEAEVG 301

Query: 294 TGEPVIV---RESGIAKHQPGQTIRISPAAGQ 322
                +V   R + +     GQ +R  PAA Q
Sbjct: 302 NDHASLVGVQRGATLYFQPKGQAVR--PAAAQ 331


Lambda     K      H
   0.321    0.138    0.396 

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: 298
Number of extensions: 11
Number of successful extensions: 3
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: 342
Length of database: 334
Length adjustment: 28
Effective length of query: 314
Effective length of database: 306
Effective search space:    96084
Effective search space used:    96084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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 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