GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF3990
          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:

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