GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatJ in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_771 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_771
          Length = 304

 Score =  598 bits (1541), Expect = e-176
 Identities = 304/304 (100%), Positives = 304/304 (100%)

Query: 1   MRIVPHILGAAIAAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGKP 60
           MRIVPHILGAAIAAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGKP
Sbjct: 1   MRIVPHILGAAIAAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGKP 60

Query: 61  VGYSHDIQLKIVEAIKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQ 120
           VGYSHDIQLKIVEAIKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQ
Sbjct: 61  VGYSHDIQLKIVEAIKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQ 120

Query: 121 QVDFSVGIFEIGTKLLSKKDSAYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVI 180
           QVDFSVGIFEIGTKLLSKKDSAYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVI
Sbjct: 121 QVDFSVGIFEIGTKLLSKKDSAYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVI 180

Query: 181 SAKDHGESFQMLETGRAVAFMMDDALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGD 240
           SAKDHGESFQMLETGRAVAFMMDDALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGD
Sbjct: 181 SAKDHGESFQMLETGRAVAFMMDDALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGD 240

Query: 241 APFKKAVDDAIIATYKSGEINKIYEKWFMQPIPPKGLNLMFPMSEELKALIANPTDKAAD 300
           APFKKAVDDAIIATYKSGEINKIYEKWFMQPIPPKGLNLMFPMSEELKALIANPTDKAAD
Sbjct: 241 APFKKAVDDAIIATYKSGEINKIYEKWFMQPIPPKGLNLMFPMSEELKALIANPTDKAAD 300

Query: 301 EKKS 304
           EKKS
Sbjct: 301 EKKS 304


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: 433
Number of extensions: 3
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: 304
Length adjustment: 27
Effective length of query: 277
Effective length of database: 277
Effective search space:    76729
Effective search space used:    76729
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