GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_836
          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 (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