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 Beta-glucosidase (EC 3.2.1.21) (characterized)
to candidate CCNA_01019 CCNA_01019 beta-glucosidase

Query= reanno::Caulo:CCNA_01019
         (758 letters)



>FitnessBrowser__Caulo:CCNA_01019
          Length = 758

 Score = 1494 bits (3867), Expect = 0.0
 Identities = 758/758 (100%), Positives = 758/758 (100%)

Query: 1   MISTTLRSLSLALLISASASALSVVPALADAAKPAAALAHPWMDKSLDADKRADLVLKAM 60
           MISTTLRSLSLALLISASASALSVVPALADAAKPAAALAHPWMDKSLDADKRADLVLKAM
Sbjct: 1   MISTTLRSLSLALLISASASALSVVPALADAAKPAAALAHPWMDKSLDADKRADLVLKAM 60

Query: 61  TNDEKFTLIFGYFGADMKPKYTRIPESLPGSAGYIAGVPRLGIPAQFQTDAGVGVATQGS 120
           TNDEKFTLIFGYFGADMKPKYTRIPESLPGSAGYIAGVPRLGIPAQFQTDAGVGVATQGS
Sbjct: 61  TNDEKFTLIFGYFGADMKPKYTRIPESLPGSAGYIAGVPRLGIPAQFQTDAGVGVATQGS 120

Query: 121 AKEFRERTALPSGMATTATWNPELAFQGGAMIGKEARDSGFNVQLAGGVNLVREPRNGRN 180
           AKEFRERTALPSGMATTATWNPELAFQGGAMIGKEARDSGFNVQLAGGVNLVREPRNGRN
Sbjct: 121 AKEFRERTALPSGMATTATWNPELAFQGGAMIGKEARDSGFNVQLAGGVNLVREPRNGRN 180

Query: 181 FEYGGEDPLLAGVMVAAQIRGIQSNNIISTIKHYALNAQETGRFVVSSNIDDTAARMSDL 240
           FEYGGEDPLLAGVMVAAQIRGIQSNNIISTIKHYALNAQETGRFVVSSNIDDTAARMSDL
Sbjct: 181 FEYGGEDPLLAGVMVAAQIRGIQSNNIISTIKHYALNAQETGRFVVSSNIDDTAARMSDL 240

Query: 241 LAFQFAIEQSDPHSVMCAYNRVNSVYACESDWLLNTVLKKDWGYKGYVMSDWGAAHSSAK 300
           LAFQFAIEQSDPHSVMCAYNRVNSVYACESDWLLNTVLKKDWGYKGYVMSDWGAAHSSAK
Sbjct: 241 LAFQFAIEQSDPHSVMCAYNRVNSVYACESDWLLNTVLKKDWGYKGYVMSDWGAAHSSAK 300

Query: 301 AANAGLDQESAGDAFDKQPFFAAPLKADLASGAVSQARIDDMARRVLRAMFASGVVDHPL 360
           AANAGLDQESAGDAFDKQPFFAAPLKADLASGAVSQARIDDMARRVLRAMFASGVVDHPL
Sbjct: 301 AANAGLDQESAGDAFDKQPFFAAPLKADLASGAVSQARIDDMARRVLRAMFASGVVDHPL 360

Query: 361 TGAPLAMPAETLAAHAKITQADAEEGIVLLKNDGGLLPLAKTAKTIAVIGSYADVGVLSG 420
           TGAPLAMPAETLAAHAKITQADAEEGIVLLKNDGGLLPLAKTAKTIAVIGSYADVGVLSG
Sbjct: 361 TGAPLAMPAETLAAHAKITQADAEEGIVLLKNDGGLLPLAKTAKTIAVIGSYADVGVLSG 420

Query: 421 GGSSQVYPVGGRAVQGLEPKTWPGPVIYYPSSPLKAIAARYPGAKVVYDDGTDPARAAKL 480
           GGSSQVYPVGGRAVQGLEPKTWPGPVIYYPSSPLKAIAARYPGAKVVYDDGTDPARAAKL
Sbjct: 421 GGSSQVYPVGGRAVQGLEPKTWPGPVIYYPSSPLKAIAARYPGAKVVYDDGTDPARAAKL 480

Query: 481 AASSDLALVFADQWTTESVDVTTLNLPKNQDATIDAVASANKKTVVVLLTGGPLLMPWLD 540
           AASSDLALVFADQWTTESVDVTTLNLPKNQDATIDAVASANKKTVVVLLTGGPLLMPWLD
Sbjct: 481 AASSDLALVFADQWTTESVDVTTLNLPKNQDATIDAVASANKKTVVVLLTGGPLLMPWLD 540

Query: 541 KVGAVVEAWFPGTAGGEAIARVLTGEVDASGRLPVTFPKSVAELPRPKLDGLGKPDGEMF 600
           KVGAVVEAWFPGTAGGEAIARVLTGEVDASGRLPVTFPKSVAELPRPKLDGLGKPDGEMF
Sbjct: 541 KVGAVVEAWFPGTAGGEAIARVLTGEVDASGRLPVTFPKSVAELPRPKLDGLGKPDGEMF 600

Query: 601 DVDYTLEGAAVGYKWYDLKKIEPLFAFGHGLSYTQFAYSNLTASASGDTLTVSFEVKNVG 660
           DVDYTLEGAAVGYKWYDLKKIEPLFAFGHGLSYTQFAYSNLTASASGDTLTVSFEVKNVG
Sbjct: 601 DVDYTLEGAAVGYKWYDLKKIEPLFAFGHGLSYTQFAYSNLTASASGDTLTVSFEVKNVG 660

Query: 661 RRPGKDVPQVYVGPKAGGWEAPKRLAGFQKVSLAPGASQRVTVTVDPRLLAVWDSKAHGW 720
           RRPGKDVPQVYVGPKAGGWEAPKRLAGFQKVSLAPGASQRVTVTVDPRLLAVWDSKAHGW
Sbjct: 661 RRPGKDVPQVYVGPKAGGWEAPKRLAGFQKVSLAPGASQRVTVTVDPRLLAVWDSKAHGW 720

Query: 721 SIAAGQYDIALGASSRAISSTAQVTLAARSLPVSPAAK 758
           SIAAGQYDIALGASSRAISSTAQVTLAARSLPVSPAAK
Sbjct: 721 SIAAGQYDIALGASSRAISSTAQVTLAARSLPVSPAAK 758


Lambda     K      H
   0.316    0.131    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: 1747
Number of extensions: 77
Number of successful extensions: 1
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: 758
Length of database: 758
Length adjustment: 40
Effective length of query: 718
Effective length of database: 718
Effective search space:   515524
Effective search space used:   515524
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