Alignments for a candidate for treF in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Pseudomonas benzenivorans DSM 8628

Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate WP_090441135.1 BLS63_RS05730 glycoside hydrolase family 15 protein

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



>NCBI__GCF_900100495.1:WP_090441135.1
          Length = 598

 Score =  238 bits (606), Expect = 8e-67
 Identities = 180/617 (29%), Positives = 280/617 (45%), Gaps = 40/617 (6%)

Query: 44  DYGFLSDCETTCLISSAGSVEWLCVPRPDSPSVFGAIL--DRGAGHFRLGPYGVSVPAAR 101
           + G + +C    L+++ G + W C P  D    F  +L  D+  G       G+S  +  
Sbjct: 9   ELGLIGNCRVAALVNTLGRLVWWCYPNFDGDPAFSRLLAGDQEKGFSDCLLDGMS-SSRS 67

Query: 102 RYLPGSLILETTWQTHTGWLIVRDALVMGPWHDIDTRSRTHRRTPMDWDAEHILLRTVRC 161
            YL  + I+ TT Q   G  +           D   R   + R          L R +  
Sbjct: 68  EYLRNTAIISTTLQDAAGNAVRIT--------DFAPRFLQYGRNFRPAQ----LCRLIEP 115

Query: 162 VSGTVELVMSCEPAFDYHRVSATWEYSGPAYGEAIARASRNPDSHPTLRLTTNLRIGIEG 221
           + G   + +   P         T  Y  P +  A +   R      T+RLTT+  +    
Sbjct: 116 LQGLPRVTLRMRP---------THGYGKPCHAVAGSSHIRYLGGADTIRLTTDAPLSYIL 166

Query: 222 REARARTRLTEGDNVFVALSWSKHPAPQTYEEAADKMWKTSEAWRQWINVGDFPDHPWRA 281
           RE      LT   ++ + +      AP+   +   K  +TS  W +W+     P   W+ 
Sbjct: 167 RETPFA--LTRPISLVMGVDEPLDDAPEELVKTFLK--RTSACWHEWVRALAIP-FEWQE 221

Query: 282 YLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWIRDSTFALWGLYTLGL 341
            + R+A+TLK   +  TGA++AA TTS+PE P  +RNWDYRY W+RD+ F +  L  LG 
Sbjct: 222 VVIRAAITLKLCNFEETGAIIAAVTTSIPEAPGSQRNWDYRYCWLRDAYFVIQALNRLGA 281

Query: 342 DREADDFFSFIADVSGANNGERHPLQVMYGVGGERSLVEEELHHLSGYDNSRPVRIGNGA 401
            R  + +  FI  V  A  G    L+ +YG+  +  L E     L+G+    PVR+GN A
Sbjct: 282 TRTMERYVDFITTV--ATGGAE--LKPLYGIVPDLDLSERIEPDLAGFLGHGPVRVGNQA 337

Query: 402 YNQRQHDIWGTMLDSV---YLHAKSREQIPDALWPVLKNQVEEAIKHWKEPDRGIWEVRG 458
             Q QHD++G+++ +V   ++  +  +   + +  +L++    A     EPD GIWE RG
Sbjct: 338 VEQIQHDVFGSVVLAVAQSFVDERLPKPGDEGMLRLLESLAARAACFAFEPDAGIWEYRG 397

Query: 459 EPQHFTSSKIMCWVALDRGSKLAELQGEKSYAQQWRAIAEEIKADVLARG-VDKRGVLTQ 517
             +  T S ++CWVA DR  ++A   G    A+ W   A  ++  +L     ++R   T 
Sbjct: 398 RQRVHTHSALLCWVACDRVGRIAARLGLAQEARTWHEEARRLRERILHDAWSERRQSFTG 457

Query: 518 RYGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGLVLRYRVEETDDGLAGEE 577
            +G D LDAS+LL      + A DPR  ATV  +  EL  +G +LRY    T D     E
Sbjct: 458 TFGHDDLDASVLLMNELGIIDAGDPRFIATVECVGRELNVNGHLLRY---ATADDFGLPE 514

Query: 578 GTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLHLYAEEIEPRTGRHLGNFPQAFT 637
             F +  FW + AL  IG    A+     L++  +   L AE++ P TG   GN PQ ++
Sbjct: 515 TAFLVVKFWYLDALAAIGRRDEARERYAELVAARNTYGLLAEDLHPHTGEMWGNIPQTYS 574

Query: 638 HLALINAVVHVIRAEEE 654
              L+N  + +  + EE
Sbjct: 575 MAGLVNTAMRLSISWEE 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: 1033
Number of extensions: 56
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: 598
Length adjustment: 38
Effective length of query: 630
Effective length of database: 560
Effective search space:   352800
Effective search space used:   352800
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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