GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Pseudomonas fluorescens FW300-N2E3

Align L-Arginine ABC transporter, ATPase component (characterized)
to candidate AO353_27990 AO353_27990 amino acid transporter

Query= reanno::pseudo6_N2E2:Pf6N2E2_5663
         (254 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_27990
          Length = 254

 Score =  441 bits (1135), Expect = e-129
 Identities = 224/254 (88%), Positives = 237/254 (93%)

Query: 1   MYKLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKI 60
           M  LE+QDLHKRYG+HEVLKGVSL+A AGDVISIIGSSGSGKSTFLRCINLLEQP++G I
Sbjct: 1   MNTLEIQDLHKRYGTHEVLKGVSLEAKAGDVISIIGSSGSGKSTFLRCINLLEQPNSGNI 60

Query: 61  LLNNEELKLVAGKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTALENIMEAPVHVLG 120
           LLN E+LKLVA K G LKAA+PKQLQRMRSRL+MVFQHFNLWSHM+ALEN+MEAPVHVLG
Sbjct: 61  LLNGEQLKLVANKTGGLKAAEPKQLQRMRSRLAMVFQHFNLWSHMSALENVMEAPVHVLG 120

Query: 121 VTKAQAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSAL 180
           + K  AREKAEHYLNKVGVAHR  AYP HMSGGEQQRVAIARALAMEPEVMLFDEPTSAL
Sbjct: 121 LDKKLAREKAEHYLNKVGVAHRMGAYPAHMSGGEQQRVAIARALAMEPEVMLFDEPTSAL 180

Query: 181 DPELVGDVLKVMQGLALEGRTMVVVTHEMGFAREVSNQLVFLHKGIVEESGNPREVLVNP 240
           DPELVG+VLKVMQ LALEGRTMVVVTHEMGFAREVSNQLVFLHKG VEE GNPREVLVNP
Sbjct: 181 DPELVGEVLKVMQDLALEGRTMVVVTHEMGFAREVSNQLVFLHKGQVEERGNPREVLVNP 240

Query: 241 QSERLQQFLSGSLK 254
           QSERLQQFL+GSLK
Sbjct: 241 QSERLQQFLAGSLK 254


Lambda     K      H
   0.317    0.133    0.372 

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: 323
Number of extensions: 8
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: 254
Length of database: 254
Length adjustment: 24
Effective length of query: 230
Effective length of database: 230
Effective search space:    52900
Effective search space used:    52900
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: 47 (22.7 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