GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapQ in Pseudomonas stutzeri RCH2

Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate GFF3103 Psest_3162 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= TCDB::Q52813
         (400 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 =  408 bits (1049), Expect = e-118
 Identities = 203/383 (53%), Positives = 273/383 (71%), Gaps = 1/383 (0%)

Query: 19  RSAMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQS 78
           RS   DP+ R+  +Q+L ++ +V F W++ HNT  NLA     SGFGFL   AGF I Q 
Sbjct: 12  RSPFTDPRIRAWVFQVLAVLAVVAFGWYLFHNTQTNLAHRGITSGFGFLNNAAGFGISQH 71

Query: 79  LITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEV 138
           LI +S   TY R   VG+LNTLLV+V GIF AT++GF++G+GRLS NWLI +L T+Y+E+
Sbjct: 72  LIDYSESDTYGRVFWVGLLNTLLVSVIGIFLATVMGFILGVGRLSSNWLIRQLATLYIEI 131

Query: 139 FRNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALV 198
           FRNIPPLL+IFF Y  V+S LP PR S+ L   +++NNRG+  P P    G  A  +AL+
Sbjct: 132 FRNIPPLLLIFFVYFAVISPLPGPRNSLSLWDVVFVNNRGVQMPAPSAGDGFWAFWLALL 191

Query: 199 IAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFN 258
           +A+VA +++ RWA  R+ ATG+ F   WT+  L + +P L+  ++G P T++VP   +FN
Sbjct: 192 VALVAVVVLNRWARARRHATGRMFPVFWTSPGLFLAIPWLMTFIAGAPFTWEVPELQRFN 251

Query: 259 LTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVV 318
           + GG VV PE +S+ +ALS YTA+FI E VR GI+ V  GQ+EAA +LGL P  V RLV+
Sbjct: 252 IRGGWVVIPELVSIVVALSVYTAAFIGETVRSGIQSVSHGQTEAAASLGLRPGQVLRLVI 311

Query: 319 VPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVY 377
           VPQALR+I+PPLTSQYLNL KNSSLA AIG+ D+V++  GT+LNQ+GQAIE + I   VY
Sbjct: 312 VPQALRVIVPPLTSQYLNLAKNSSLAAAIGYPDMVSLFAGTVLNQTGQAIETMAITMSVY 371

Query: 378 LSLSILTSLFMNWFNAKMALVER 400
           L++SI  SL MNW+N ++AL+ER
Sbjct: 372 LAISISISLLMNWYNKRIALIER 394


Lambda     K      H
   0.327    0.141    0.432 

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: 539
Number of extensions: 17
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: 400
Length of database: 394
Length adjustment: 31
Effective length of query: 369
Effective length of database: 363
Effective search space:   133947
Effective search space used:   133947
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: 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