GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Pseudomonas fluorescens GW456-L13

Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate PfGW456L13_2346 glutamine ABC transporter ATP-binding component

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773
         (244 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2346
          Length = 515

 Score =  229 bits (583), Expect = 1e-64
 Identities = 126/243 (51%), Positives = 165/243 (67%), Gaps = 8/243 (3%)

Query: 1   MISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 60
           ++ +K+I K YG  QVL      V+ G+V+ + GPSGSGK++LI+ VN LE    GDI++
Sbjct: 260 ILQLKNIQKSYGTHQVLMGIDLNVEYGQVVSIIGPSGSGKTSLIRTVNGLETIDTGDILL 319

Query: 61  DGTSI--ADPKTNLPKLRS---RVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATK 115
            G     A  K N  +LR     +GMVFQ+F LFPH TI +N+T+A  +  G+  E +  
Sbjct: 320 FGEKFIEASDKPNSTRLRKGVRHIGMVFQNFNLFPHRTILDNVTLAP-RYHGQPGELSEH 378

Query: 116 KGLQLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEV 175
           +   LL++VGL AHAHK+P QLSGGQQQRVAIARALAM+P +MLFDEPTSALDPE+VN+V
Sbjct: 379 RAYALLDKVGLLAHAHKYPHQLSGGQQQRVAIARALAMEPQIMLFDEPTSALDPELVNDV 438

Query: 176 LDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAERTQ 235
           L+V+  LA EGMTM+ VTHEM FA  ++DRV+FM+ G I  D   E    D  A  ER +
Sbjct: 439 LNVIRDLAKEGMTMLIVTHEMDFAMSISDRVVFMENGNIQLDAAPETIRCD--AEGERVR 496

Query: 236 HFL 238
            F+
Sbjct: 497 RFM 499


Lambda     K      H
   0.321    0.136    0.394 

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: 289
Number of extensions: 9
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: 244
Length of database: 515
Length adjustment: 29
Effective length of query: 215
Effective length of database: 486
Effective search space:   104490
Effective search space used:   104490
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