GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsA in Pseudomonas stutzeri RCH2

Align GtsA (GLcE), component of Glucose porter, GtsABCD (characterized)
to candidate GFF1857 Psest_1896 ABC-type sugar transport system, periplasmic component

Query= TCDB::Q88P38
         (428 letters)



>FitnessBrowser__psRCH2:GFF1857
          Length = 415

 Score =  517 bits (1332), Expect = e-151
 Identities = 267/428 (62%), Positives = 316/428 (73%), Gaps = 13/428 (3%)

Query: 1   MNSTLRLAAAISFASLIPLGAQAADAKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFIWK 60
           MN+  RLA ++S A  +P+ A A    G VEV+HWWTSGGEK A D L+  VE+ G  WK
Sbjct: 1   MNAFHRLALSVSLA--LPVLAHA----GEVEVLHWWTSGGEKRAADTLQKLVEQKGHSWK 54

Query: 61  DGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQDWAATGLLDADVLKDVAKEGKWD 120
           D AVAGGGG  AMTVLK+RAV+GNPP  AQIKGPDIQ+W   GLL    L D AK  +WD
Sbjct: 55  DFAVAGGGGEAAMTVLKTRAVSGNPPSAAQIKGPDIQEWGELGLLAN--LDDTAKAERWD 112

Query: 121 SLLDKKVADTVKYDGDYVAVPVNIHRINWLWINPEVFKKAGIDKAPTTLDEFYAAADKLK 180
           +LL ++V   ++YDG YVAVPVN+HR+NWLWINPEVF+KAG  K P TLDEF+AAADKLK
Sbjct: 113 ALLPEQVRKIMQYDGSYVAVPVNVHRVNWLWINPEVFEKAGA-KPPKTLDEFFAAADKLK 171

Query: 181 AAGFIPLAHGGQPWQDSTVFESVVLSVMGVDGYKKALVDLDSATLTGPQMVKALTELKKV 240
           AAGFIP+AHGGQPWQD TVFE  VLS++G D Y KA V+LD+ TLTG +MV+A T LKK+
Sbjct: 172 AAGFIPVAHGGQPWQDGTVFEGFVLSILGPDDYHKAFVELDNDTLTGDKMVQAFTALKKL 231

Query: 241 ATYMDPDGKGQDWNLEAAKVINGKAGMQIMGDWAKSEWTLAKKTAGKDYQCVPFPGTDKS 300
             Y+D D  G++WN     VI+GKAGMQIMGDWAKSE+T A K AGK+YQC+PFPGT  S
Sbjct: 232 RDYIDADAAGREWNRATGMVIDGKAGMQIMGDWAKSEFTAANKVAGKNYQCLPFPGTQGS 291

Query: 301 FLYNIDSLVVFKQNNAGTSAGQQDIARKVLGEDFQKVFSINKGSIPVRNDMLADMGKYGF 360
           F +NIDSL +FK ++      Q+D+AR VL  +FQ  F+ NKGSIPVR D   DM +  F
Sbjct: 292 FAFNIDSLAMFKLSSDDNRKAQEDLARTVLEPEFQTFFNQNKGSIPVRQDQ--DMSE--F 347

Query: 361 DACAQTSAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADAAKKL 420
           DACAQ S  DF   AK  GLQPS+ H MA +  VQGA FDVVTN+ NDPKADP  AAK+L
Sbjct: 348 DACAQQSMTDFKEAAKGSGLQPSLTHGMAASSYVQGAVFDVVTNFFNDPKADPQKAAKQL 407

Query: 421 AAAIKAAQ 428
           AAAIKA Q
Sbjct: 408 AAAIKAVQ 415


Lambda     K      H
   0.315    0.131    0.392 

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: 556
Number of extensions: 21
Number of successful extensions: 4
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: 428
Length of database: 415
Length adjustment: 32
Effective length of query: 396
Effective length of database: 383
Effective search space:   151668
Effective search space used:   151668
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 (21.6 bits)
S2: 50 (23.9 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