GapMind for catabolism of small carbon sources

 

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

Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate AO353_25420 AO353_25420 spermidine/putrescine ABC transporter ATP-binding protein

Query= TCDB::Q88P35
         (384 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25420
          Length = 372

 Score =  242 bits (617), Expect = 1e-68
 Identities = 152/369 (41%), Positives = 206/369 (55%), Gaps = 17/369 (4%)

Query: 4   LELRNVNKTYG---SGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60
           + +R V K YG   SG P  LK I L I+D EF  L+GPSGCGK+TL+  IAG E  T G
Sbjct: 12  VSIRAVRKVYGDPHSG-PVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPTQG 70

Query: 61  AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKI----RKLPQAAIDEEV 116
            IL+  ++++   P  R +  VFQ YAL+P M++ EN+ FGL+     + L +A I E V
Sbjct: 71  EILLYGENIADRPPYQRPVNTVFQHYALFPHMTIAENLAFGLESHPMGKVLSKAQIAERV 130

Query: 117 ARVAKLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176
             +  L+Q+E    R+P QLSGGQQQRVA+ RALA  PK+ L DEPLS LD KLR  MR 
Sbjct: 131 REMLALVQMERFATRRPTQLSGGQQQRVALARALAPHPKVLLLDEPLSALDLKLRQAMRE 190

Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFI 236
           E+K +  +   T ++VTHDQ EA+T+ D++AV+ +G +QQ G P+ IY  P N+FVA FI
Sbjct: 191 ELKAIQAKTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYERPRNRFVADFI 250

Query: 237 GSPPMNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQIALGAA 296
           G    NFI   +   +  L     +G A   LP    +D   G  + L +RPE++ L  A
Sbjct: 251 GE--TNFIEGTVTHVEAGLAWF--AGPAGHPLPAQPCSDVNVGATVALSVRPERLHLLPA 306

Query: 297 DGNGLPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGDTLNLQFDPARVLL 356
           + +G    R + Q+    G DL   V+LN      RL       V  +L         LL
Sbjct: 307 NTDGALPCRIDAQIY--LGTDLQYQVSLNDGS---RLTVRTPNSVDQSLRFAVGSQAGLL 361

Query: 357 FDAANGERL 365
           FD  +   L
Sbjct: 362 FDRGSASVL 370


Lambda     K      H
   0.320    0.137    0.391 

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: 360
Number of extensions: 14
Number of successful extensions: 2
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: 384
Length of database: 372
Length adjustment: 30
Effective length of query: 354
Effective length of database: 342
Effective search space:   121068
Effective search space used:   121068
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 (21.8 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