GapMind for catabolism of small carbon sources

 

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

Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate Pf1N1B4_153 Glucoamylase (EC 3.2.1.3)

Query= CAZy::ABK72415.1
         (668 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_153
          Length = 607

 Score =  371 bits (952), Expect = e-107
 Identities = 237/607 (39%), Positives = 324/607 (53%), Gaps = 37/607 (6%)

Query: 45  YGFLSDCETTCLISSAGSVEWLCVPRPDSPSVFGAILDRG-AGHFRLGPYGVSVPAARR- 102
           +G + D  +  L++  GSV++ C P  DSPS+F A+LD   AG F+L P    +P ARR 
Sbjct: 14  HGIIGDMRSAALVNDKGSVDFFCWPEFDSPSIFCALLDSPEAGIFQLAP---DLPDARRE 70

Query: 103 --YLPGSLILETTWQTHTGWLIVRDALVMGPWHDIDTRSRTHRRTPMDWDAEHILLRTVR 160
             YLP + +L+T W +    + V D L +G   D           PM       L+R VR
Sbjct: 71  QIYLPDTNVLQTRWMSDHAVVEVTDLLPIGDSED---------DLPM-------LMRRVR 114

Query: 161 CVSGTVELVMSCEPAFDYHRVSATWEYSGPAYGEAIARASR-NPDSHPTLRLTTNLRIGI 219
            VSG   + M C    DY R         P    A  R+        P ++L +N  + I
Sbjct: 115 VVSGQATIRMRCAVRHDYARA--------PTKARARDRSVYFEATGQPAMQLCSNQSLRI 166

Query: 220 EGREARARTRLTEGDNVFVALSWSKHPAPQTYEEAADKMWKTSEAWRQWINVGDFPDHPW 279
           EG  A A   L E D     L      A      AA  + +T + WR WI   ++    W
Sbjct: 167 EGHAAVAEFIL-EQDQSAEFLLGGVDDARFKEGAAALCLERTLKFWRDWIGQSNYRGR-W 224

Query: 280 RAYLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWIRDSTFALWGLYTL 339
           R  + RSAL LK LT    GA+LAA T  LPETP GERNWDYRY+WIRD++F ++    L
Sbjct: 225 REMVNRSALALKLLTSRKHGAILAAATFGLPETPGGERNWDYRYTWIRDASFTVYAFMRL 284

Query: 340 GLDREADDFFSFIADVSGANNGERHPLQVMYGVGGERSLVEEELHHLSGYDNSRPVRIGN 399
           G   EA+ +  ++       +G+   L ++Y + G + L E EL HL+G+  + PVRIGN
Sbjct: 285 GFVEEANAYTRWLRGRVRDCHGKTMKLNILYAIDGRQELPEVELPHLAGHGGATPVRIGN 344

Query: 400 GAYNQRQHDIWGTMLDSVYLHAKSREQIPDALWPVLKNQVEEAIKHWKEPDRGIWEVRGE 459
            AY+Q Q DI+G ++D+VYL  K  E I    W      V++  + W++ D GIWE+RGE
Sbjct: 345 QAYDQIQLDIFGELMDAVYLVNKHGEAISHEGWKHTVEVVDQVCETWQQKDVGIWEMRGE 404

Query: 460 PQHFTSSKIMCWVALDRGSKLAELQGEKSYAQQWRAIAEEIKADVLAR-GVDKRGVLTQR 518
             HF  S++MCWVA+DR  +LA  +   +   +W    + I AD+ +    ++RG   Q 
Sbjct: 405 QYHFLHSRLMCWVAVDRAIRLASKRSLPAPFARWDQTRQAIYADIWSNFWNEERGHFVQH 464

Query: 519 YGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGLVLRYRVEETD-DGLAGEE 577
            G   LD S+LL  L RF+ A DPR  AT+ AI   L   G+V RYR +++  DGL G E
Sbjct: 465 IGGTGLDGSMLLMPLVRFVSAKDPRWIATLEAIEKSLVRAGMVYRYRNDDSQIDGLPGTE 524

Query: 578 GTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLHLYAEEIEPRTGRHLGNFPQAFT 637
           G F  CSFW V  L   G++ +A    E+LL +A+PL LYAEE +    RHLGN PQA T
Sbjct: 525 GAFAACSFWYVECLARAGQVEKAHLEFEQLLKYANPLGLYAEEFDSH-ARHLGNTPQALT 583

Query: 638 HLALINA 644
           HLALI+A
Sbjct: 584 HLALISA 590


Lambda     K      H
   0.319    0.135    0.426 

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: 1121
Number of extensions: 44
Number of successful extensions: 7
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: 668
Length of database: 607
Length adjustment: 38
Effective length of query: 630
Effective length of database: 569
Effective search space:   358470
Effective search space used:   358470
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 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