GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AO353_21725 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate Pf1N1B4_5642 ABC-type polar amino acid transport system, ATPase component

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5642 ABC-type polar amino
           acid transport system, ATPase component
          Length = 263

 Score =  498 bits (1282), Expect = e-146
 Identities = 256/265 (96%), Positives = 259/265 (97%), Gaps = 2/265 (0%)

Query: 1   MTQAQVSTQNASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRC 60
           MTQAQVSTQN  QALL+IR LHKQYG LEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRC
Sbjct: 1   MTQAQVSTQN--QALLDIRGLHKQYGQLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRC 58

Query: 61  VNMLEEFQGGQILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQ 120
           VNMLEEFQGGQILLDGESIGYHEVNGKRVRH EKVIA+HRAMTGMAFQQFNLFPHLTALQ
Sbjct: 59  VNMLEEFQGGQILLDGESIGYHEVNGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQ 118

Query: 121 NVTLGLLKVKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPS 180
           NVTLGLLKVKKLHKDEAV LAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPS
Sbjct: 119 NVTLGLLKVKKLHKDEAVALAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPS 178

Query: 181 LMLFDEVTSALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEE 240
           LMLFDEVTSALDPELVGEVL+VIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEE
Sbjct: 179 LMLFDEVTSALDPELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEE 238

Query: 241 QGPPKELFERPQSPRLAEFLKNTRF 265
           QGPPKELFERPQSPRLAEFLKNTRF
Sbjct: 239 QGPPKELFERPQSPRLAEFLKNTRF 263


Lambda     K      H
   0.319    0.135    0.379 

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: 339
Number of extensions: 6
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: 265
Length of database: 263
Length adjustment: 25
Effective length of query: 240
Effective length of database: 238
Effective search space:    57120
Effective search space used:    57120
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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