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 alpha,alpha-trehalase (EC 3.2.1.28) (characterized)
to candidate BPHYT_RS26585 BPHYT_RS26585 trehalase

Query= BRENDA::Q3BXX2
         (557 letters)



>FitnessBrowser__BFirm:BPHYT_RS26585
          Length = 557

 Score =  590 bits (1521), Expect = e-173
 Identities = 292/502 (58%), Positives = 353/502 (70%), Gaps = 6/502 (1%)

Query: 41  PTPPTPDLAYPELFQAVQRGELFDDQKHFVDFLPLRDPALINADYLAQHDHPGFDLRKFV 100
           P PP PD  Y +LF AVQ  +++ DQK FVD  P  DPA I   Y  Q  +PGF L KFV
Sbjct: 57  PLPPAPDKLYGDLFVAVQTAQIYPDQKTFVDATPNADPAAIVQLYEQQKHNPGFSLAKFV 116

Query: 101 DANFEE-SPPVQTDAIRQDTALREHIDLLWPKLVRSQNHVPPHSSLLALPHPYVVPGGRF 159
           +  F   S PV T    Q   LREHI+ LWP L R+    PP+SSL+ LP PYVVPGGRF
Sbjct: 117 NKYFTPPSEPVITPPANQ--TLREHINWLWPALTRTTTSAPPNSSLIPLPKPYVVPGGRF 174

Query: 160 REVYYWDSYFTMLGLVKSGETTLSRQMLDNFAYLIDTYGHIPNGNRTYYLSRSQPPFFSY 219
           RE YYWD+YFTMLGL +SG   L   MLDNFAY IDT+GHIPNGNRTYYL RSQPPFFS+
Sbjct: 175 REGYYWDTYFTMLGLQESGNENLVDDMLDNFAYEIDTFGHIPNGNRTYYLDRSQPPFFSH 234

Query: 220 MVELQAGVEGEAVYQRYLPQLQKEYAYWMQGSDDLQPGQAARHVVRLADGSVLNRYWDER 279
           MVEL A +EG  VYQ+YLP L+KEYAYWMQG    +PG A R+VV + D +VLNRYWDE 
Sbjct: 235 MVELAAKMEGHGVYQKYLPALRKEYAYWMQGESTTRPGSATRNVVVMPDRTVLNRYWDEL 294

Query: 280 DTPRPEAWLHDTRTAAEVKDRPAAEVYRDLRAGAESGWDYTSRWLADGQNLRTIRTTAIL 339
           DTPR E++L D +TA +   R   +VYR+LRA AESGWD++SRW  D   L T+RTT+I+
Sbjct: 295 DTPRDESYLEDIQTAQQASGRNPNDVYRELRATAESGWDFSSRWFGDNMTLATVRTTSII 354

Query: 340 PIDLNSLLYHLERTLAQACAQA-GAECTRDYAALAQQRKQAIDAHLWNAAGYYADYDWQT 398
           P+DLNSL++HLE T+A+ C +     C  ++A  A +R   I+ +LWN  GYY DYDWQ 
Sbjct: 355 PVDLNSLMFHLEITIAKGCGETRDFRCVGEFAQRAAKRALGINRYLWNPNGYYGDYDWQL 414

Query: 399 RTLSNQVTAAALYPLFAGLASDDHAKRTASTVRKTLLRPGGLATTAVKTGQQWDEPNGWA 458
               +  TAA ++PLF G A  D A +TA  V+ TLL+PGGL TT   T QQWD PNGWA
Sbjct: 415 ARPRDNKTAAMVFPLFVGAAWPDRALKTAKQVQSTLLQPGGLVTTTYNTTQQWDAPNGWA 474

Query: 459 PLQWVAVDGLRRYGEDALARTIGERFLAQVQALFAREHKLVEKYGLE-TDAAGGGGGEYA 517
           PL W A+ GL+RYG+DALA+ IG RFL+ V+ ++A + KLVEKY +E +   GGGGGEY 
Sbjct: 475 PLHWAAIQGLKRYGQDALAQQIGTRFLSDVKGVYASDQKLVEKYVVEGSGTGGGGGGEYP 534

Query: 518 LQDGFGWTNGVTLMLLNLY-PG 538
           LQDGFGWTNGVTL LL+LY PG
Sbjct: 535 LQDGFGWTNGVTLKLLDLYSPG 556


Lambda     K      H
   0.319    0.135    0.420 

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: 860
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 557
Length of database: 557
Length adjustment: 36
Effective length of query: 521
Effective length of database: 521
Effective search space:   271441
Effective search space used:   271441
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 (21.8 bits)
S2: 53 (25.0 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

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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:

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