GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate GFF3990 Psest_4063 sulfate ABC transporter, ATP-binding protein

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__psRCH2:GFF3990
          Length = 334

 Score =  217 bits (553), Expect = 3e-61
 Identities = 130/311 (41%), Positives = 186/311 (59%), Gaps = 17/311 (5%)

Query: 3   TLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAI 62
           ++E+ ++NK +G      L  I L I+ GE + L+GPSGCGK++L+  IAGLET   G+I
Sbjct: 2   SIEISHINKRFGQF--QALNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSI 59

Query: 63  MIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVAR---- 118
           +   +DVS    +DR++  VFQ YAL+  M+V EN+ FGL+++   Q   +A +A     
Sbjct: 60  VFHGEDVSSRDVRDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEKVHE 119

Query: 119 VAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178
           +  L+Q++ L +R P QLSGGQ+QR+A+ RALA  PK+ L DEP   LDAK+R E+R  +
Sbjct: 120 LLGLVQLDWLADRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWL 179

Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGS 238
             +H+ +  T+V+VTHDQ EAM + D++ VM  G+I+Q GTP E+Y NPA++FV  F+G 
Sbjct: 180 ARLHEDVHLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEVYANPASEFVYDFLGD 239

Query: 239 PPMNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDV-ILGLRPEQIMLAAGE 297
                   RLQ  D R V       A    A+    AG E RD+  LG      +  AG+
Sbjct: 240 AN------RLQLDDQRSVLFRPHEVALSREAVAEHLAG-EVRDIRPLGALTRVTLKVAGQ 292

Query: 298 GDSASSIRAEV 308
              A  I AEV
Sbjct: 293 ---AEPIEAEV 300


Lambda     K      H
   0.318    0.135    0.382 

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: 330
Number of extensions: 15
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: 386
Length of database: 334
Length adjustment: 29
Effective length of query: 357
Effective length of database: 305
Effective search space:   108885
Effective search space used:   108885
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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