Alignments for a candidate for bgl in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Caulobacter crescentus NA1000

Align c84_2 (EC 3.2.1.21|3.2.1.37) (characterized)
to candidate CCNA_03149 CCNA_03149 beta-glucosidase/beta-xylosidase

Query= CAZy::AGU12029.1
         (798 letters)



>FitnessBrowser__Caulo:CCNA_03149
          Length = 806

 Score = 1080 bits (2792), Expect = 0.0
 Identities = 531/803 (66%), Positives = 638/803 (79%), Gaps = 8/803 (0%)

Query: 3   IKRREFLASMGSIAGLAVVPGAASAAANTKPAASA--LYKQASAPIKARVEDLLGRMTLE 60
           + RR F AS+ +++  A +P  A AA      +    LYK  + P+ AR++DLL RMTLE
Sbjct: 5   LTRRLFGASLAALSA-AALPSLAQAAGQAPKTSGGKPLYKDPTQPVDARIQDLLSRMTLE 63

Query: 61  EKIAQMQCVWLKKATLQNEDTSFNGEKAASAYPNGMGMFARPSDRRLDKP-----AAAGD 115
           EK AQ+  +WL KA +Q  +  F+ E+A+  +P+G+G  +RPSDR+  KP     AAAG 
Sbjct: 64  EKAAQLIGIWLTKAKIQTPEGEFSAEQASKNFPHGLGQISRPSDRKGAKPVTVIGAAAGA 123

Query: 116 SGEQANRGPKETADYVNAVQKWAMESTRLGIPVMMHEEALHGYVARESTNFPQAIGLASS 175
                NR   ETA Y NA QKWA+E TRLGIP++MH+EALHGYVAR++T+FPQ+I LAS+
Sbjct: 124 DDGAINRNAAETARYTNAAQKWAIEKTRLGIPLLMHDEALHGYVARDATSFPQSIALAST 183

Query: 176 FDPVLVEKVYSVAAREMRARGTHLALAPVVDVAREPRWGRIEETYGEDPHLCGVMGKASV 235
           FD  L EK+++VAAREMRARG++LALAPVVDVAR+PRWGRIEETYGEDPHLC  +G AS+
Sbjct: 184 FDTELTEKIFAVAAREMRARGSNLALAPVVDVARDPRWGRIEETYGEDPHLCAEIGLASI 243

Query: 236 IGFSGNTLPLAKDKVLATLKHMTGHGQPESGTNIGPANVGERTLREDFFPPFEKIIRETK 295
            GF G TLPLAKDKV  TLKHMTGHGQPE+GTN+GPA + ERTLRE+FFPPFE+ + E  
Sbjct: 244 RGFQGATLPLAKDKVFVTLKHMTGHGQPENGTNVGPAQIAERTLRENFFPPFERAVTELP 303

Query: 296 IAAVMPSYNEIDGIPSHANRWLLTDVLRKEWGFEGVTVSDYMAVAELISRHHLAGTPKEA 355
           + AVMPSYNEIDG+PSHANRWLLT +LR+EWG++G   SDY A+ E+ISRH L     E 
Sbjct: 304 VRAVMPSYNEIDGVPSHANRWLLTKILREEWGYKGSIQSDYFAIKEMISRHKLTSDLGET 363

Query: 356 ALQAVKAGVDIETPDPLGYLTIAELVREGKISTKEIDAAVRRVLKLKFEAGLFENPYADA 415
           A+ A++AGVD+E PD   Y  I ELV+ G+I   E+DAAV RVL++KF+AGLFENPY D 
Sbjct: 364 AVMAMRAGVDVELPDGEAYALIPELVKAGRIPQFEVDAAVARVLEMKFQAGLFENPYCDE 423

Query: 416 ARADALTATPDAIALALEAGRRSAVLLKNDKGLLPLNGKKVGKLLLLGTHAKSTPIGGYS 475
             ADA TATPDA+ALA EA R+S VLLKNDKGLLPL+GKK  ++ LLGTHAK TPIGGYS
Sbjct: 424 KTADAKTATPDAVALAREAARKSVVLLKNDKGLLPLDGKKFKRMALLGTHAKDTPIGGYS 483

Query: 476 DIPRHVVSVHEGLEKEAKAQGFQLSYSEGVRLTEGHVWGKDEIVFTKPEVNQRLIAEAVE 535
           DIPRHVVS+HEGL  EAKAQGF L Y+E VR+TE  +W +D + FT P VN +LIAEAVE
Sbjct: 484 DIPRHVVSIHEGLTAEAKAQGFALDYAEAVRITEQRIWAQDAVNFTDPAVNAKLIAEAVE 543

Query: 536 AAKKADTIVMVLGDNEQTAREAWADNHLGDRTTLDLLGQQNDLARAIFALNKPTVVLLLN 595
            AKKAD +VMVLGDNEQT+REAWAD+HLGDR +LDL+GQQNDLARAIF L KPTVV LLN
Sbjct: 544 VAKKADIVVMVLGDNEQTSREAWADHHLGDRDSLDLMGQQNDLARAIFDLGKPTVVFLLN 603

Query: 596 GRPLSATLLAERADALLECWYLGQETGHAVADLLFGRANPGGKLPVTIAREPGQLPMFYN 655
           GRPLS  LL ERADA++E WYLGQETGHA AD+LFGRANPGGKLPV+IAR+ GQLP++YN
Sbjct: 604 GRPLSINLLKERADAIIEGWYLGQETGHAAADVLFGRANPGGKLPVSIARDVGQLPVYYN 663

Query: 656 RKPSTRRGYIDGVTTPLYPFGFGLSYTRFEISAPRLEQARISTSGSTRVQVDVKNVGGVA 715
           RKP+ RRGY+DG TTPLYPFGFGLSYT F++SAPRL +A+I    + +V+VDV N G VA
Sbjct: 664 RKPTARRGYLDGETTPLYPFGFGLSYTTFDVSAPRLAKAKIGQGETVKVEVDVTNTGKVA 723

Query: 716 GDEVVQLYIRDDVSSVTRPLLELKGFNRVTLQPGEQKTVSFDIKPTDLWFYNADMKRVVE 775
           GDEVVQLY+ D+ +SVTRP+LELK F RVTL PG + TV+F+IKP+DLW +N DMKRVVE
Sbjct: 724 GDEVVQLYVHDEAASVTRPVLELKHFKRVTLAPGAKTTVTFEIKPSDLWMWNLDMKRVVE 783

Query: 776 PGTFTIYAGPNSVDLKKTTLTVA 798
           PG F+I  GPNSVDLKKTTLTVA
Sbjct: 784 PGDFSILVGPNSVDLKKTTLTVA 806


Lambda     K      H
   0.316    0.133    0.385 

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: 1590
Number of extensions: 46
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: 798
Length of database: 806
Length adjustment: 41
Effective length of query: 757
Effective length of database: 765
Effective search space:   579105
Effective search space used:   579105
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 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