GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF3103
          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 (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