Alignments for a candidate for ams in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for ams in Echinicola vietnamensis KMM 6221, DSM 17526

Align β-fructofuranosidase (BT3082;BT_3082) (EC 3.2.1.26|3.2.1.64|3.2.1.80) (characterized)
to candidate Echvi_2807 Echvi_2807 Beta-fructosidases (levanase/invertase)

Query= CAZy::AAO78188.1
         (548 letters)



>FitnessBrowser__Cola:Echvi_2807
          Length = 548

 Score =  794 bits (2050), Expect = 0.0
 Identities = 369/544 (67%), Positives = 439/544 (80%), Gaps = 3/544 (0%)

Query: 6   RTVLTLFVLSFSC-LAAIAGEVSFKITKQYLNFPISHKENRGRMTFEVNGKPDLSVVIRL 64
           + +L + +L  +C    +A E+  KITK+YLNFPIS +E R +MTF+  G+P+L++VIRL
Sbjct: 6   QNILLVVLLLLTCHFTVLASEIELKITKRYLNFPISGQEARHKMTFQSEGQPELNIVIRL 65

Query: 65  APDEAEYWVFKDVSAFKGKTIKITYDGNEKGLSKIYQSDEIEGQAELYKEKNRPQFHFTT 124
           A  E +YWVFKDVS   GKT+ I+Y+GN+ GLSKIYQ+DEI G   LY+E+NRPQFHFTT
Sbjct: 66  AAGEPDYWVFKDVSNLIGKTLTISYEGNQAGLSKIYQADEIAGADSLYQEQNRPQFHFTT 125

Query: 125 RRGWINDPNGLIYYEGEYHLFYQHNPFERDWENMHWGHAVSKDLIHWTELPDALYPDHLG 184
           RRGWINDPNGL+YY+GEYHLFYQHNP+ER+WENMHWGHAVS DLIHW ELPDALYPD LG
Sbjct: 126 RRGWINDPNGLLYYDGEYHLFYQHNPYEREWENMHWGHAVSNDLIHWKELPDALYPDELG 185

Query: 185 TMFSGSAVIDYDNTAGFNKGKTPAMVAAFTAASSDRQVQGIAYSLDKGRTFTKYDKNPVI 244
           TMFSGSAVID  NTAG+N G TPAMVAA+TAA+ DRQ QGIAYSLDKG+TFTKY+ NPVI
Sbjct: 186 TMFSGSAVIDDQNTAGWNSGSTPAMVAAYTAANRDRQTQGIAYSLDKGKTFTKYEGNPVI 245

Query: 245 NSKEKWNSQDTRDPKVFWYAPSKHWVLVLNERDGHSIYTSSNLKDWKYESHVTGFWECPE 304
           +SKEKWNS DTRDPKVFWY P  HWV+VLNERDGHSIY SS+LK+W+Y+SH TGFWECPE
Sbjct: 246 DSKEKWNSIDTRDPKVFWYEPGNHWVMVLNERDGHSIYNSSDLKNWEYQSHTTGFWECPE 305

Query: 305 LFELPVDGDKNHTKWVMYGATGTYMLGSFDGKVFTPEAGKYCYTTGSIYAAQTFTNIPAS 364
           LFELPVDG+ +   WVMYGA+GTYMLG F+GK FTP  GK+ Y TGSIYAAQTFTN+P  
Sbjct: 306 LFELPVDGNTDEMHWVMYGASGTYMLGEFNGKTFTPTTGKHHYITGSIYAAQTFTNVP-- 363

Query: 365 DGRRIQIGWGRISHPGMPFNGMMMLPTELTLRTTKDGIRLVNVPVKEVESLCKPLRSWKS 424
           +GRRIQ+GWG+ISHPGMPF GMMMLPTELTLRTTKDG RL N PVKE E+L  P+  W+ 
Sbjct: 364 NGRRIQMGWGQISHPGMPFTGMMMLPTELTLRTTKDGPRLFNEPVKETENLFIPIGQWRD 423

Query: 425 LSSDEANRHLKEFYDADCLRIKTTIKLSHATDAGFNLFGQRMIGYDMNSNTLNGRFYSPQ 484
           L+++EAN+ L+       LRI+T IKLSHAT AG +L GQR++ YD+N N LNG FYSP 
Sbjct: 424 LTAEEANKILEAHSAKSTLRIRTRIKLSHATSAGISLSGQRILNYDLNYNKLNGAFYSPN 483

Query: 485 DPTSMELSADIYIDRTSIEVFIDGGLYSYSMERRPDTNNREGLHFWGNRIEVKDLQVFSV 544
           DPT M +SADIYID+TSIE+F+D G ++  M R     N E L FWGN I ++ L++  V
Sbjct: 484 DPTEMGISADIYIDKTSIEIFVDDGAFTVVMPRETVEKNNEHLRFWGNNISIQSLEILDV 543

Query: 545 ESIW 548
            SIW
Sbjct: 544 ASIW 547


Lambda     K      H
   0.318    0.135    0.423 

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: 1182
Number of extensions: 50
Number of successful extensions: 2
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: 548
Length of database: 548
Length adjustment: 36
Effective length of query: 512
Effective length of database: 512
Effective search space:   262144
Effective search space used:   262144
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: 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)
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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