GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Dinoroseobacter shibae DFL-12

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 3606889 Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q52813
         (400 letters)



>FitnessBrowser__Dino:3606889
          Length = 411

 Score =  290 bits (742), Expect = 5e-83
 Identities = 165/386 (42%), Positives = 227/386 (58%), Gaps = 9/386 (2%)

Query: 24  DPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFS 83
           D +YR   +Q + ++ L+ F  W+  N   NLA       F FL   A +EI Q+LI ++
Sbjct: 26  DTRYRGYTFQFIALIALIFFFGWLVSNAIYNLAALGQDINFSFLGQPASYEIDQTLIPYT 85

Query: 84  SDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIP 143
           S  T+ RA  VG+LNTLLVA  G  TATI G L G+ RLS+NWL+AK+ +VYVE+FRNIP
Sbjct: 86  STDTHMRAAFVGLLNTLLVAFLGCITATIFGVLAGVLRLSKNWLVAKVMSVYVEIFRNIP 145

Query: 144 PLLVIFFWYLGVLSVLPQPRESVG--------LPFSMYLNNRGLAFPKPIFDTGMIAVGI 195
            L+ I      +   LPQPR   G        L  S+   NRG+  P P+++ G   V  
Sbjct: 146 VLIWIVIISAVMSQALPQPRAFRGEDATATMVLWDSVAFTNRGVYIPAPVWNPGSGIVVA 205

Query: 196 ALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAG 255
             V++I+   +  R+A      TG+       ++A+     LL F V G P+  D P  G
Sbjct: 206 VFVLSIIGIFVFRRYAKNLLFNTGKLLPVGRISLAIFFVPTLLAFFVMGRPIGLDYPELG 265

Query: 256 KFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTR 315
            FN  GG  +    ++L+ AL+ YT +FIAE VR GI  V KGQ+EAA ALG+ P+ +  
Sbjct: 266 GFNFRGGINIRGTLIALWFALALYTGAFIAENVRAGILAVSKGQTEAAAALGMRPNRIMS 325

Query: 316 LVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLV-AVGGTILNQSGQAIEIVCIWG 374
           L+++PQALR+IIPP+ SQYLNLTKNSSLA AIG+ DL   +GG  LNQ+G++ E V +  
Sbjct: 326 LIILPQALRVIIPPVISQYLNLTKNSSLAAAIGYMDLTGTLGGVTLNQTGRSFECVLLLM 385

Query: 375 IVYLSLSILTSLFMNWFNAKMALVER 400
           + YL +S+  S  MN +N  + L ER
Sbjct: 386 LFYLLISLSISALMNLYNNAVKLKER 411


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: 498
Number of extensions: 20
Number of successful extensions: 3
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: 411
Length adjustment: 31
Effective length of query: 369
Effective length of database: 380
Effective search space:   140220
Effective search space used:   140220
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.

Links

Downloads

Related tools

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