Alignments for a candidate for treF in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Burkholderia phytofirmans PsJN

Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate BPHYT_RS06100 BPHYT_RS06100 glucoamylase

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



>FitnessBrowser__BFirm:BPHYT_RS06100
          Length = 626

 Score =  367 bits (943), Expect = e-106
 Identities = 230/617 (37%), Positives = 328/617 (53%), Gaps = 35/617 (5%)

Query: 42  IADYGFLSDCETTCLISSAGSVEWLCVPRPDSPSVFGAILDRGA-GHFRLGPYGVSVPA- 99
           I DY  + D  T  L+S  GSV+WLC PR DS + F A+L     G + + P   + P  
Sbjct: 5   IEDYALIGDGHTAALVSRDGSVDWLCWPRFDSGACFAALLGTPENGRWLIAPVSDTPPTI 64

Query: 100 ARRYLPGSLILETTWQTHTGWLIVRDALVMGP-WHDIDTRSRTHRRTPMDWDAEHILLRT 158
            RRY   +LILET ++T  G + + D +  G  W +                    ++R 
Sbjct: 65  TRRYRGETLILETDFETPEGAITLIDFMPPGNGWSE--------------------MVRL 104

Query: 159 VRCVSGTVELVMSCEPAFDYHRVSATWEYSGPAYGEAIARASRNPDSHPTLRLTTNLRIG 218
           V    GTV + M     FDY   S  W        ++  +A   PD   T  L T + + 
Sbjct: 105 VVGRRGTVRMKMELVLRFDYG-FSVPWV--DRLTHDSGIKAIVGPD---TAVLRTPVELR 158

Query: 219 IEGREARARTRLTEGDNVFVALSWS-KHPAPQTYEEAADKMWKTSEAWRQWINVGDFPDH 277
            E  +  A   ++EG+ V  +L+++  H       +    + +T   W +W +     + 
Sbjct: 159 GEDMKTVAEFTVSEGERVPFSLAYAASHLRIPPARDPHTSLARTENHWLEW-SARSTVEG 217

Query: 278 PWRAYLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWIRDSTFALWGLY 337
            W   ++RS +TLK L Y PTG ++AAPTTSLPE   G RNWDYRY W+RD+T  L  + 
Sbjct: 218 RWAEPIRRSLITLKALAYEPTGGIVAAPTTSLPEQLGGTRNWDYRYCWLRDATITLLAMM 277

Query: 338 TLGLDREADDFFSFIADVSGANNGERHPLQVMYGVGGERSLVEEELHHLSGYDNSRPVRI 397
             G   EA  + S++  V     G    LQ+MYG+ GER L E E+  L GY +++PVRI
Sbjct: 278 RGGYYDEARAWRSWLGRVMA---GAPDQLQIMYGIAGERRLPEFEIDWLRGYQDAKPVRI 334

Query: 398 GNGAYNQRQHDIWGTMLDSVYLHAKSREQIPDALWPVLKNQVEEAIKHWKEPDRGIWEVR 457
           GN A  QRQ D++G ++++++L      Q  D  W V +  ++     W+EPD GIWE R
Sbjct: 335 GNNAVGQRQLDVYGEVMNALHLARVGGLQADDTAWNVQRALLKHLDTIWQEPDEGIWETR 394

Query: 458 GEPQHFTSSKIMCWVALDRGSKLAELQGEKSYAQQWRAIAEEIKADVLARGVDKR-GVLT 516
           G  QHFT SK+M WVA DR  K AE+   +    +WRA   +I A+V  +  +      +
Sbjct: 395 GGRQHFTFSKVMAWVAYDRAIKSAEMFELEGPLDEWRATRAQIHAEVCEKAWNPALNAFS 454

Query: 517 QRYGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGLVLRYRVEETDDGLAGE 576
           Q YG D LDAS+LL  L  FLP  DPR++ TV AI  +L  DG V+RYR  E DDGL   
Sbjct: 455 QCYGTDQLDASVLLMPLVAFLPPHDPRVKGTVAAIERDLMHDGFVMRYRTTEYDDGLPPG 514

Query: 577 EGTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLHLYAEEIEPRTGRHLGNFPQAF 636
           EGTF  CSFW+V  L   G +  A  + ERLL+  + + L AEE +P   R +GNFPQAF
Sbjct: 515 EGTFLACSFWMVDNLALQGRLDEAIAMYERLLALCNDVGLLAEEYDPAAKRLVGNFPQAF 574

Query: 637 THLALINAVVHVIRAEE 653
           +H+AL++  +++++ E+
Sbjct: 575 SHVALVHTGLNLMKHEQ 591


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: 1284
Number of extensions: 68
Number of successful extensions: 5
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: 626
Length adjustment: 38
Effective length of query: 630
Effective length of database: 588
Effective search space:   370440
Effective search space used:   370440
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources