GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate AO356_28585 AO356_28585 ABC transporter

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_28585
          Length = 379

 Score =  298 bits (763), Expect = 2e-85
 Identities = 163/364 (44%), Positives = 229/364 (62%), Gaps = 21/364 (5%)

Query: 4   LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63
           L+L NVNK  G      L+++ L I  GEF++ VGPSGCGKSTL+  IAGL++I GG ++
Sbjct: 4   LKLDNVNKQLGGAR--ILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLL 61

Query: 64  IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123
           I  + V+ + P++R + MVFQSYALYP MSV +NI FGLK+ K  +  +   V + A++L
Sbjct: 62  IDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTAQIL 121

Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
           Q++ LL RKP +LSGGQ+QRVAMGRA+AR P I LFDEPLSNLDA LRV+MR E+  +H 
Sbjct: 122 QLDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHG 181

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243
           RL +T +YVTHDQ+EAMTL DK+ V+  G I+Q G+P+E+Y  PA++FVA F+GSP MNF
Sbjct: 182 RLGSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYERPASRFVAGFLGSPRMNF 241

Query: 244 V------PLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGE 297
           +      P    + +  ++ +         LA NT         + LG+RPE I L A +
Sbjct: 242 LAAFLHTPGETSQVESLVLGMTSLPFDSSGLAANT--------QLSLGIRPEHIALKAAQ 293

Query: 298 GDSASSIRAEVQVTEPTGPDTLVFVQL-NDTKVCCRLAPDVAPQVGETLTLQFDPSKVLL 356
           G +  ++       E  G +T V +    D  + CR   +   +VG+ + LQ D   + +
Sbjct: 294 GTAGIAVSG----VEYLGSETYVHLDTGQDDPMVCRCEVNAGWRVGDRVELQLDIDNLHV 349

Query: 357 FDAN 360
           FD +
Sbjct: 350 FDTH 353


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: 394
Number of extensions: 18
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: 386
Length of database: 379
Length adjustment: 30
Effective length of query: 356
Effective length of database: 349
Effective search space:   124244
Effective search space used:   124244
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: 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