Alignments for a candidate for treF in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Paraburkholderia bryophila 376MFSha3.1

Align alpha,alpha-trehalase (EC 3.2.1.28) (characterized)
to candidate H281DRAFT_02853 H281DRAFT_02853 alpha,alpha-trehalase

Query= BRENDA::Q3BXX2
         (557 letters)



>FitnessBrowser__Burk376:H281DRAFT_02853
          Length = 564

 Score =  584 bits (1505), Expect = e-171
 Identities = 288/501 (57%), Positives = 352/501 (70%), Gaps = 6/501 (1%)

Query: 43  PPTPDLAYPELFQAVQRGELFDDQKHFVDFLPLRDPALINADYLAQHDHPGFDLRKFVDA 102
           PP PD+ Y +LF AVQ  +++ DQK FVD  P  DPA+I   Y  Q   PGF L  FV+ 
Sbjct: 66  PPAPDILYGDLFVAVQTAQIYPDQKTFVDATPNADPAVIVQLYQQQRGKPGFSLANFVNQ 125

Query: 103 NFEE-SPPVQTDAIRQDTALREHIDLLWPKLVRSQNHVPPHSSLLALPHPYVVPGGRFRE 161
            F   S PV T    Q   LREHI+ LWP L R+    PP+SSL+ LP PYVVPGGRFRE
Sbjct: 126 YFTPPSEPVITPPANQ--TLREHINWLWPALTRTTTSAPPNSSLIPLPKPYVVPGGRFRE 183

Query: 162 VYYWDSYFTMLGLVKSGETTLSRQMLDNFAYLIDTYGHIPNGNRTYYLSRSQPPFFSYMV 221
            YYWD+YFTMLGL ++G   L   MLDNFAY+IDT+GHIPNGNRTYYL RSQPPFFS+MV
Sbjct: 184 GYYWDTYFTMLGLQEAGREDLVDNMLDNFAYMIDTFGHIPNGNRTYYLDRSQPPFFSHMV 243

Query: 222 ELQAGVEGEAVYQRYLPQLQKEYAYWMQGSDDLQPGQAARHVVRLADGSVLNRYWDERDT 281
           EL A VEG  VYQ+YLP L+KEY YWMQG      G A R+VV + D +VLNRYWDE DT
Sbjct: 244 ELAAKVEGHGVYQKYLPALRKEYGYWMQGEKSTPAGSATRNVVVMPDRTVLNRYWDELDT 303

Query: 282 PRPEAWLHDTRTAAEVKDRPAAEVYRDLRAGAESGWDYTSRWLADGQNLRTIRTTAILPI 341
           PR E++L D +TA +   R   +VYR+LRA AESGWD++SRW  D   L T+RTT+I+P+
Sbjct: 304 PRDESYLEDIQTAQKATGRNPNDVYRELRATAESGWDFSSRWFGDNMTLATVRTTSIIPV 363

Query: 342 DLNSLLYHLERTLAQACAQA-GAECTRDYAALAQQRKQAIDAHLWNAAGYYADYDWQTRT 400
           DLNSL++HLE ++A+ C++     C  ++A  A +R   I+ +LWN  GYY DYDWQ   
Sbjct: 364 DLNSLMFHLEISIAKGCSETRDFRCVGEFAGRAAKRALGINRYLWNPNGYYGDYDWQLAK 423

Query: 401 LSNQVTAAALYPLFAGLASDDHAKRTASTVRKTLLRPGGLATTAVKTGQQWDEPNGWAPL 460
             +  TAA ++PLF G A  + A++TA  V+ TLL+PGGLATT   T QQWD PNGWAPL
Sbjct: 424 PRDNKTAAMVFPLFVGAAWPERAQKTAQQVQSTLLQPGGLATTTYNTTQQWDAPNGWAPL 483

Query: 461 QWVAVDGLRRYGEDALARTIGERFLAQVQALFAREHKLVEKYGLE-TDAAGGGGGEYALQ 519
            WVA+ GL+RYG DALA+ IG RFL  V+ ++A + KLVEKY +E     GGGGGEY LQ
Sbjct: 484 HWVAIQGLKRYGHDALAQQIGTRFLTDVKGVYASDKKLVEKYVVEGAGTGGGGGGEYPLQ 543

Query: 520 DGFGWTNGVTLMLLNLY-PGK 539
           DGFGWTNGVTL LL+LY PG+
Sbjct: 544 DGFGWTNGVTLKLLDLYSPGE 564


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: 863
Number of extensions: 25
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: 557
Length of database: 564
Length adjustment: 36
Effective length of query: 521
Effective length of database: 528
Effective search space:   275088
Effective search space used:   275088
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.

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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