GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatJ in Pseudomonas simiae WCS417

Align ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized)
to candidate GFF5184 PS417_26550 ABC transporter

Query= reanno::pseudo1_N1B4:Pf1N1B4_771
         (304 letters)



>FitnessBrowser__WCS417:GFF5184
          Length = 300

 Score =  335 bits (858), Expect = 1e-96
 Identities = 171/271 (63%), Positives = 202/271 (74%)

Query: 24  AELTGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYSHDIQLKIVEAIKKDLDMPN 83
           A L GTL KI  + +ITLG+RDAS+PFSY+ D SGKP+GYS ++  KIVE I++   +  
Sbjct: 24  APLDGTLGKIASAKSITLGYRDASVPFSYVGDNSGKPMGYSVELASKIVERIQQKTGVAT 83

Query: 84  LQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQQVDFSVGIFEIGTKLLSKKDSAY 143
           L VKYNLVTSQTRIPLVQNGTVD+ECGST    ERQ+QV FS G   +  +LL+ KDS  
Sbjct: 84  LNVKYNLVTSQTRIPLVQNGTVDLECGSTGVTAERQKQVAFSYGFIYVKGQLLTAKDSGI 143

Query: 144 KDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVISAKDHGESFQMLETGRAVAFMMD 203
           K F DL GKNVVTTAGTT+ER LKS NA+ +  M VISAKDHGE+F+MLETGRA AF MD
Sbjct: 144 KGFPDLAGKNVVTTAGTTNERFLKSYNAEHKTNMFVISAKDHGEAFKMLETGRAAAFYMD 203

Query: 204 DALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGDAPFKKAVDDAIIATYKSGEINKI 263
           DALL GE AKAK P +W V G  QS EIY CM+RK D  F   V++ +   Y+SGEIN I
Sbjct: 204 DALLYGERAKAKDPHNWVVVGEEQSREIYSCMLRKDDPQFLAVVNETLGDLYRSGEINGI 263

Query: 264 YEKWFMQPIPPKGLNLMFPMSEELKALIANP 294
           Y++WF  PIPPKGLNL FPM+ ELKA+IA P
Sbjct: 264 YQRWFESPIPPKGLNLEFPMTRELKAIIAKP 294


Lambda     K      H
   0.315    0.131    0.365 

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: 285
Number of extensions: 9
Number of successful extensions: 1
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: 304
Length of database: 300
Length adjustment: 27
Effective length of query: 277
Effective length of database: 273
Effective search space:    75621
Effective search space used:    75621
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: 48 (23.1 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