Alignments for a candidate for bgl in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Dyella japonica UNC79MFTsu3.2

Align Beta-glucosidase (EC 3.2.1.21) (characterized)
to candidate N515DRAFT_3019 N515DRAFT_3019 beta-glucosidase

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



>FitnessBrowser__Dyella79:N515DRAFT_3019
          Length = 737

 Score =  719 bits (1856), Expect = 0.0
 Identities = 373/718 (51%), Positives = 476/718 (66%), Gaps = 15/718 (2%)

Query: 39  AHPWMDKSLDADKRADLVLKAMTNDEKFTLIFGYFGADMKPKYTRIPESLPGSAGYIAGV 98
           A PW D  L  D RAD +L  +T DEKF LI  YF    KP+   +P    GSAGYI  +
Sbjct: 31  ARPWSDPKLSPDLRADQLLAQLTQDEKFHLIRSYFAGPRKPEDKPVPPGYIGSAGYIPAL 90

Query: 99  PRLGIPAQFQTDAGVGVATQGSAKEFRERTALPSGMATTATWNPELAFQGGAMIGKEARD 158
            R+GIPA  ++DAG+GVA+    +     T LP+G  T ATW+P++AF+GGAMIG EA  
Sbjct: 91  ERVGIPAIQESDAGLGVASSERMRPGDYATPLPAGPVTAATWDPKVAFRGGAMIGGEAHA 150

Query: 159 SGFNVQLAGGVNLVREPRNGRNFEYGGEDPLLAGVMVAAQIRGIQSNNIISTIKHYALNA 218
            GFNV LAGG NL+REPRNGRNFEY GEDPLLAG MV   IRGI+S +++STIKH+ALN 
Sbjct: 151 KGFNVLLAGGTNLMREPRNGRNFEYAGEDPLLAGTMVGEAIRGIESQHVVSTIKHFALND 210

Query: 219 QETGRFVVSSNIDDTAARMSDLLAFQFAIEQSDPHSVMCAYNRVNSVYACESDWLLNTVL 278
           QET R  V   I + A R SDLLAF+ AIE+  P SVMC+YN++N  +ACE+D+LLN VL
Sbjct: 211 QETARTTVDVRIGEQAMRESDLLAFELAIERGKPGSVMCSYNKLNGDWACENDYLLNQVL 270

Query: 279 KKDWGYKGYVMSDWGAAHSSAKAANAGLDQESAGDAFDKQPFFAAPLKADLASGAVSQAR 338
           K+DW Y G+VMSDWG  HS+AKA NAGLDQESA + FDK  +F  PL+  LA G V QAR
Sbjct: 271 KRDWKYPGFVMSDWGGVHSAAKAVNAGLDQESAAEIFDKDIYFDKPLRDALAKGEVKQAR 330

Query: 339 IDDMARRVLRAMFASGVVDHPLTGAPLAMPAETLAAHAKITQADAEEGIVLLKNDGGLLP 398
           IDDM RR+LR+ FA+GV +HP   AP+   A    A   +     E G VLL+ND  LLP
Sbjct: 331 IDDMVRRILRSFFAAGVFEHPAKKAPIDEKANLAVARETL-----EAGAVLLRNDNQLLP 385

Query: 399 L-AKTAKTIAVIGSYADVGVLSGGGSSQVYPVGGRAVQGLEPKTWPGPVIYYPSSPLKAI 457
           L     ++IAVIG++AD GVL+GGGSS V   GG AV GL+P  WPGPV+Y+P SPLKA+
Sbjct: 386 LDVARLESIAVIGAHADKGVLAGGGSSLVTAKGGNAVPGLKPSDWPGPVMYHPYSPLKAL 445

Query: 458 AARYPGAKVVYDDGTDPARAAKLAASSDLALVFADQWTTESVDVTTLNLPKNQDATIDAV 517
            +  P AKV +  G D A AA LAA S +A+VF  +W  E  D   L+LP  QDA + AV
Sbjct: 446 QSMAPKAKVQFTGGDDVAAAAALAAKSQVAVVFVQKWAGEDFDARDLSLPDGQDALVTAV 505

Query: 518 ASANKKTVVVLLTGGPLLMPWLDKVGAVVEAWFPGTAGGEAIARVLTGEVDASGRLPVTF 577
           A AN +T+VVL  G P+ MPWL++VGAV+E W+PG   G  IA +L+G+V+ SGRLP+++
Sbjct: 506 AKANPRTIVVLENGSPVAMPWLEQVGAVLEVWYPGGDAGNGIANLLSGKVNPSGRLPLSW 565

Query: 578 PKSVAELPRPKLDGLGKPDGEMFDVDYTLEGAAVGYKWYDLKKIEPLFAFGHGLSYTQFA 637
           P+ V +LPRP+L G G        VDY +EGA VGY+WY  K ++PLF FG+GLSYT F 
Sbjct: 566 PRDVLQLPRPELPGAGGSGALPQSVDYAIEGANVGYRWYQSKDLQPLFPFGYGLSYTSFE 625

Query: 638 YSNLTASASGDTLTVSFEVKNVGRRPGKDVPQVYV---GPKAGGWEAPKRLAGFQKVSLA 694
           +  L        +T +  V+N G+R G DV QVYV   G KA      +RLAGF KV L 
Sbjct: 626 HGALKVDTKDGKVTATVTVRNTGKRAGADVAQVYVQVPGAKA------RRLAGFSKVFLK 679

Query: 695 PGASQRVTVTVDPRLLAVWDSKAHGWSIAAGQYDIALGASSRAISSTAQVTLAARSLP 752
           PG  + +++ ++ +LLA +D+  HGW +  G+Y ++ G SS  +   A V L+A  LP
Sbjct: 680 PGEQRELSIPLERKLLADFDTARHGWVVRGGEYVVSEGRSSADLGRPAAVQLSAGVLP 737


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: 1469
Number of extensions: 67
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: 758
Length of database: 737
Length adjustment: 40
Effective length of query: 718
Effective length of database: 697
Effective search space:   500446
Effective search space used:   500446
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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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