GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5403 in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate GFF3103 Psest_3162 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= reanno::pseudo6_N2E2:Pf6N2E2_5403
         (375 letters)



>lcl|FitnessBrowser__psRCH2:GFF3103 Psest_3162 amine acid ABC
           transporter, permease protein, 3-TM region,
           His/Glu/Gln/Arg/opine family
          Length = 394

 Score =  528 bits (1359), Expect = e-154
 Identities = 258/375 (68%), Positives = 309/375 (82%)

Query: 1   VRAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEAD 60
           +RAWVFQV+ V+AV+A GW+LF NTQTNL HRGITSGFGFL  +AGFGI+QHLIDY+E+D
Sbjct: 20  IRAWVFQVLAVLAVVAFGWYLFHNTQTNLAHRGITSGFGFLNNAAGFGISQHLIDYSESD 79

Query: 61  SYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLL 120
           +Y RVF +GLLNTLLV+ IG+ LAT++GFI+GV RLS NW+I +LAT+Y+E+FRNIPPLL
Sbjct: 80  TYGRVFWVGLLNTLLVSVIGIFLATVMGFILGVGRLSSNWLIRQLATLYIEIFRNIPPLL 139

Query: 121 QILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVL 180
            I F YFAV   +PGPR + +  D  FV++RG+ MPA    +GFW F +++++A+VA+V+
Sbjct: 140 LIFFVYFAVISPLPGPRNSLSLWDVVFVNNRGVQMPAPSAGDGFWAFWLALLVALVAVVV 199

Query: 181 MTRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVLI 240
           + RWA  R  ATG  F  FW    LFL IP L   + GAP  WE+PEL+ FN  GGWV+I
Sbjct: 200 LNRWARARRHATGRMFPVFWTSPGLFLAIPWLMTFIAGAPFTWEVPELQRFNIRGGWVVI 259

Query: 241 PELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVI 300
           PEL+++ +AL+VYTAAFI E VRSGI+SVSHGQTEAA SLGLR G  LR VI+PQALRVI
Sbjct: 260 PELVSIVVALSVYTAAFIGETVRSGIQSVSHGQTEAAASLGLRPGQVLRLVIVPQALRVI 319

Query: 301 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS 360
           +PPLTSQYLNLAKNSSLAA IGYP+MVSLFAGTVLNQTGQAIE +AITMSVYLAISISIS
Sbjct: 320 VPPLTSQYLNLAKNSSLAAAIGYPDMVSLFAGTVLNQTGQAIETMAITMSVYLAISISIS 379

Query: 361 LLMNWYNKRIALIER 375
           LLMNWYNKRIALIER
Sbjct: 380 LLMNWYNKRIALIER 394


Lambda     K      H
   0.328    0.141    0.430 

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: 557
Number of extensions: 15
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: 375
Length of database: 394
Length adjustment: 30
Effective length of query: 345
Effective length of database: 364
Effective search space:   125580
Effective search space used:   125580
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 (21.8 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 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