GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntT in Pseudomonas fluorescens FW300-N1B4

Align gluconate:H+ symporter (gntT) (characterized)
to candidate Pf1N1B4_5074 Gluconate permease

Query= reanno::BFirm:BPHYT_RS16725
         (465 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5074
          Length = 470

 Score =  295 bits (756), Expect = 2e-84
 Identities = 165/466 (35%), Positives = 253/466 (54%), Gaps = 24/466 (5%)

Query: 20  LILLITRYKVYPFLVLIIVSLLLGLASGMPMATIVKSFETGNGNTLGHIAIVVGLGTMLG 79
           L+ L+ +YK  PF+ L++VS+L+ L +G+  A +V + E G G TLGHIAI++ LG M+G
Sbjct: 1   LLFLVLKYKFQPFVALMLVSILVALVAGVKPADLVATIEGGMGKTLGHIAIIIALGAMIG 60

Query: 80  KMMAESGGAERIATTLIDFFGEKNIHWAMMIVAIIVGLPVFFEVGFVLLIPIAFNVAKRT 139
           +++  SGGAE +A TLI  FG +    A+ I   +VG+PVFFEVG ++L+P+A+ VA+  
Sbjct: 61  RIIELSGGAEALAKTLITRFGNRRTPLALTIAGFMVGVPVFFEVGVIILMPLAYGVARSA 120

Query: 140 NKSLLLVGLPMVAGLSVVHGLLPPHPAAMLAVQAYHADIGRTIAYGLIVGVPTAIVAGPL 199
            K LL+  LPM A L  VH  LPPHP A+ A     AD+GR + +GL +      V   +
Sbjct: 121 RKPLLVFALPMCAALLTVHAFLPPHPGAVAAASQLGADLGRVLMFGLPITAFLCYVGYRV 180

Query: 200 FALMISRYIKLPKE-----------NALAAQFLGHGDETKNGAQTAAQNVA--------- 239
              M  R   +  +           N   A +    D++   A  AA ++          
Sbjct: 181 AGRMTRRVYPMTDDIRAEVYGPHVTNEDLAAWSNGNDKSPERAAVAASHMGLEEATSSIV 240

Query: 240 ---PKRELPSFGITLLTILLPVILMLVGSWADLFTTPKTLPNDLLHFAGNSDVALLIAVL 296
              P    P FG+ +  I+LP+IL+L+G+ +       ++   ++   G   VALLI  L
Sbjct: 241 SKLPPAPPPGFGLIVSLIVLPIILILLGTLSTSLLPADSVLRGIMTVLGAPLVALLIDTL 300

Query: 297 VSFWTFGASRGFTREQIQKFCGDCLAPIAGITLIVGAGGGFGRVLMDSGISKEIVNVATA 356
           +  W  G+ RG++R Q+    G  L  +A + LI GAGG FG+VL+D+GI   + ++   
Sbjct: 301 LCAWLLGSRRGWSRTQVSDVIGSALPGVAMVILIAGAGGVFGKVLVDTGIGAVVSDMLRT 360

Query: 357 MHLSPLLFGWLVAALIRLATGSATVAMTTACGIVAP-IASASGVHVEPELLVLATGSGSL 415
             L  L  G+L+  L+R   GS TVA+ T  GI++P I +         LL LA G G L
Sbjct: 361 TGLPVLALGFLLTMLLRAVQGSTTVALVTTAGIISPLIVTLDLTANHMALLCLAMGGGGL 420

Query: 416 IFSHVNDGGFWLIKEYFGMTVGQTFKTWSLLETIISLMGLGLTFAL 461
             SH+ND G+W+  +  G+ V    +TW++L T++  +G G+T  +
Sbjct: 421 AMSHINDAGYWIFTKLSGLNVADGLRTWTVLTTLLGTLGFGITLLI 466


Lambda     K      H
   0.326    0.141    0.417 

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: 616
Number of extensions: 32
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: 465
Length of database: 470
Length adjustment: 33
Effective length of query: 432
Effective length of database: 437
Effective search space:   188784
Effective search space used:   188784
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 (21.6 bits)
S2: 51 (24.3 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