GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF2244
          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.

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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