GapMind for catabolism of small carbon sources

 

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

Align Trehalose permease IIC protein (characterized, see rationale)
to candidate Pf1N1B4_836 PTS system, trehalose-specific IIB component (EC 2.7.1.69) / PTS system, trehalose-specific IIC component (EC 2.7.1.69)

Query= uniprot:A0A0N9WDQ5
         (480 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_836 PTS system,
           trehalose-specific IIB component (EC 2.7.1.69) / PTS
           system, trehalose-specific IIC component (EC 2.7.1.69)
          Length = 480

 Score =  882 bits (2279), Expect = 0.0
 Identities = 448/480 (93%), Positives = 463/480 (96%)

Query: 1   MSHDYPTIASELLHSLGGADNLEQAAHCVTRLRLALKDPQRVDSATLNQIDLVKGSFFTG 60
           MSHDYP I +ELLHSLGG+DNLEQAAHCVTRLRLALKDP  VDSATLNQIDLVKGSF+TG
Sbjct: 1   MSHDYPNIVTELLHSLGGSDNLEQAAHCVTRLRLALKDPSLVDSATLNQIDLVKGSFYTG 60

Query: 61  GLFQVVIGPGEVEKVYAALRQQTGLAASTIADVKQKGADKTNAMQRLVRVFSDVFMPILP 120
           GLFQVVIGPGEVEKVYA LR+QTGLA STIADVKQK ADK + MQRLVRVFSDVFMPILP
Sbjct: 61  GLFQVVIGPGEVEKVYAELRRQTGLAVSTIADVKQKSADKIHPMQRLVRVFSDVFMPILP 120

Query: 121 ALIIAGLLMGVNNLIGAKGMFIAGKTLLEAYPTLDGVWSLINLMANTSFVFLPALVGWSA 180
           ALIIAGLLMG+NNLIGAKGMFI GKTLL+AYP LDG+WSLINLMANTSFVFLPALVGWSA
Sbjct: 121 ALIIAGLLMGINNLIGAKGMFIEGKTLLDAYPKLDGLWSLINLMANTSFVFLPALVGWSA 180

Query: 181 AKRFGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGLDGQSLPYFDIFGWFKIEKVGYQGQ 240
           AKRFGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGL+GQSLPYFDI G F+IEKVGYQGQ
Sbjct: 181 AKRFGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGLEGQSLPYFDILGMFQIEKVGYQGQ 240

Query: 241 ILPILMAAYVMSVIEKWLRARVPNAIQLLVVPITTIVVTGVLALAVIGPVTRHLGILITE 300
           ILPILMAAYVMSVIEKWLRARVPNA+QLLVVPITTIVVTGVLALAVIGPVTRHLGILITE
Sbjct: 241 ILPILMAAYVMSVIEKWLRARVPNAVQLLVVPITTIVVTGVLALAVIGPVTRHLGILITE 300

Query: 301 GVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQ 360
           GVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQ
Sbjct: 301 GVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQ 360

Query: 361 GSAALGVFYMTRSARDKSMASTSAISAYFGITEPAMFGVNLRYKFPFYAALSGSALGCMF 420
           GSAAL VFYMTRS RDKSMASTSAISAYFGITEPAMFGVNLRYKFPFYAAL GSALGC+F
Sbjct: 361 GSAALAVFYMTRSVRDKSMASTSAISAYFGITEPAMFGVNLRYKFPFYAALIGSALGCIF 420

Query: 421 LSLNKVQASAIGVGGLPGFISIIPQFIPMFIVGMVIAMVVPFVLTCGMSMKIVRAGYRVA 480
           LSLNKVQASAIGVGGLPGFISIIPQFIPMF+VGMVIAMVVPFVLTCG+SM+IVR GYRVA
Sbjct: 421 LSLNKVQASAIGVGGLPGFISIIPQFIPMFVVGMVIAMVVPFVLTCGLSMRIVRPGYRVA 480


Lambda     K      H
   0.326    0.141    0.419 

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: 905
Number of extensions: 27
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: 480
Length of database: 480
Length adjustment: 34
Effective length of query: 446
Effective length of database: 446
Effective search space:   198916
Effective search space used:   198916
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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