GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5404 in Escherichia coli BW25113

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate 17340 b3270 putative transport system permease protein (VIMSS)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>FitnessBrowser__Keio:17340
          Length = 367

 Score =  503 bits (1296), Expect = e-147
 Identities = 233/355 (65%), Positives = 290/355 (81%)

Query: 8   PDMPPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRA 67
           P  P   +S   + W+R N+FSSW N+LLT+   +L++ ++PPL+ WA L ANWVG+TRA
Sbjct: 9   PPRPASHNSSRAMVWVRKNLFSSWSNSLLTIGCIWLMWELIPPLLNWAFLQANWVGSTRA 68

Query: 68  DCTKEGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFPRKAIYGLS 127
           DCTK GACWVFI +RFGQFMYG YP D RWR++L + + ++ +AP+F    P +  Y  +
Sbjct: 69  DCTKAGACWVFIHERFGQFMYGLYPHDQRWRINLALLIGLVSIAPMFWKILPHRGRYIAA 128

Query: 128 FLVLYPISAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNM 187
           + V+YP+  W L++GG F L+ V T QWGGL LTL+IA+VGI GALP GI+LALGRRS+M
Sbjct: 129 WAVIYPLIVWWLMYGGFFALERVETRQWGGLTLTLIIASVGIAGALPWGILLALGRRSHM 188

Query: 188 PAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIAE 247
           P +R++ V FIEFWRGVPLITVLFMSSVMLPLF+ EG + DKL+RAL+GVILFQSAY+AE
Sbjct: 189 PIVRILSVIFIEFWRGVPLITVLFMSSVMLPLFMAEGTSIDKLIRALVGVILFQSAYVAE 248

Query: 248 VVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVII 307
           VVRGGLQA+PKGQYEAA ++ LGYW++ GLVILPQALKLVIPG+VNT IALFKDTSLVII
Sbjct: 249 VVRGGLQALPKGQYEAAESLALGYWKTQGLVILPQALKLVIPGLVNTIIALFKDTSLVII 308

Query: 308 IGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTG 362
           IGLFDL +SV+QA  DP WLGM+TEGYVFAAL++WIFCF MSRYS +LE++ +TG
Sbjct: 309 IGLFDLFSSVQQATVDPAWLGMSTEGYVFAALIYWIFCFSMSRYSQYLEKRFNTG 363


Lambda     K      H
   0.330    0.144    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: 698
Number of extensions: 27
Number of successful extensions: 1
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: 365
Length of database: 367
Length adjustment: 30
Effective length of query: 335
Effective length of database: 337
Effective search space:   112895
Effective search space used:   112895
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 (21.9 bits)
S2: 49 (23.5 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