GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapM in Marinobacter adhaerens HP15

Align AapM, 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 GFF2244 HP15_2194 amino acid ABC transporter, permease protein

Query= TCDB::Q52814
         (384 letters)



>lcl|FitnessBrowser__Marino:GFF2244 HP15_2194 amino acid ABC
           transporter, permease protein
          Length = 362

 Score =  370 bits (951), Expect = e-107
 Identities = 193/359 (53%), Positives = 252/359 (70%), Gaps = 16/359 (4%)

Query: 27  VAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLFIQAVWSGPDRTFCATTLQGGIQP 86
           V W+R NL +   + +LT+    L+  +V  L+NW F+ A + G D + C          
Sbjct: 17  VKWMRENLFSGWFNTVLTLGVAYLLVTSVGPLLNWFFLDANFVGSDPSACTG-------- 68

Query: 87  DGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGILFILLLVPMLIPSAP-RKGLNAIL 145
              +GACW FIS + + FI+G YP   +WR  ++ +L  +  VP  I   P RK L    
Sbjct: 69  ---AGACWLFISQRLNFFIYGFYPDELQWRVDVMFLLLAVSFVPQFIERFPGRKWLGLFG 125

Query: 146 LFAVLPVIAFWLLHGG-FGLEVVETPLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRM 204
           +F  LP++ ++L+ GG FGLE V++  WGGLM+TL+L+++GI  SLP+GILLALGRRS M
Sbjct: 126 IFG-LPIVGYFLIPGGSFGLEEVQSSKWGGLMLTLILAYIGIIASLPIGILLALGRRSDM 184

Query: 205 PVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLRALIGVSIFTSAYMAE 264
           P+IR +CV FIEV R VPLITVLFMASVMLPLFLP G N +KL RALIG++++ SAYMAE
Sbjct: 185 PIIRGICVVFIEVWRAVPLITVLFMASVMLPLFLPEGVNFEKLARALIGITLWQSAYMAE 244

Query: 265 VIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTI 324
           VIRGGLQAIP+GQ+E AD+LGLGYW+K  L+I+PQA+K+VIP IVNTFI  FKDT+LV I
Sbjct: 245 VIRGGLQAIPRGQYEAADALGLGYWRKMGLVILPQALKMVIPGIVNTFISLFKDTTLVLI 304

Query: 325 IGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGFMERHLDTGHK 383
           IG+FD+LG V+   +D  W +    I G +F  F FW+FCFG+SRYS  +ER LDTGHK
Sbjct: 305 IGLFDILGTVQSTVTDPAWQNVA--IEGYVFVAFCFWVFCFGISRYSQNLERKLDTGHK 361


Lambda     K      H
   0.330    0.145    0.469 

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: 595
Number of extensions: 35
Number of successful extensions: 4
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: 384
Length of database: 362
Length adjustment: 30
Effective length of query: 354
Effective length of database: 332
Effective search space:   117528
Effective search space used:   117528
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.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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