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_3248 N515DRAFT_3248 exo-1,4-beta-glucosidase (EC 3.2.1.74)

Query= reanno::Korea:Ga0059261_1166
         (834 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3248
          Length = 838

 Score =  811 bits (2094), Expect = 0.0
 Identities = 434/839 (51%), Positives = 542/839 (64%), Gaps = 28/839 (3%)

Query: 12  RLLSSAMLASLPVVMAATASARDDAAQAHPAMWPERRPTVPLDPAVELRVADLLAKMSLE 71
           R+   A+  +L  +    A A D A   HP  WP  +  +P + A+E RVA+L+AKMS+E
Sbjct: 9   RIAPIALAIALACLPLGAAPAADTAV--HPEQWPAAKWPLPRNAALEQRVAELMAKMSVE 66

Query: 72  QKVGQIIQADIASVTPADVHRYHLGSVLNGGNSDPGGRYNAPPRDWLAAADAFYAASMQP 131
           +KVGQ+IQADI++VTP DV +Y LGS+L GGNS P G+  A    W A ADAF+ A+M  
Sbjct: 67  EKVGQLIQADISAVTPEDVRKYRLGSILAGGNSKPEGKTTATAEQWKALADAFHRAAMDT 126

Query: 132 NGALPRIPVIWGSDAVHGHNNVVGATLFPHNIGLGAARNPDLIRRIGEATAIEMRVTGLD 191
           +G    IP++ G DAVHGHNN VGATLFP N  LGA R+P LIR IG ATA E+R TG++
Sbjct: 127 SGGHQAIPLLIGIDAVHGHNNTVGATLFPQNSALGATRDPQLIREIGAATAAEVRATGIN 186

Query: 192 WTFAPTLAVVRDDRWGRTYEGFGETPEIATAYAAPLIEGLQGKIGDKDWLRGPHIIATAK 251
           WTFAPTLAV +D RWGR+YEG+ + P++   YA+ +IEGLQGK G   +L   H+IA+AK
Sbjct: 187 WTFAPTLAVPQDLRWGRSYEGYSQDPKVVAQYASAMIEGLQGKAGTPKFLDASHVIASAK 246

Query: 252 HFLGDGGTRNGKDQGDTEIGEAGLRDLFSPPYLPALDAGVQSVMVSFSGWNGAKMHGNKS 311
           HFL DGGT++GKDQGD ++ E  LR++ +  Y PA+DAGVQ+VM SFS WNG KMHGNK+
Sbjct: 247 HFLADGGTKDGKDQGDAQVSETELREVHAAGYPPAIDAGVQTVMASFSSWNGQKMHGNKA 306

Query: 312 LLTGVVKQRWNFDGFLVGDWNGHGQVAGCTATNCPQSAIAGLDMYMAPDSWKALYEATLG 371
           LLT V+K R +F GF+VGDWNGHGQV GC+ T+CP S  AG+DM MAPDSW+ LYE TL 
Sbjct: 307 LLTDVLKGRMDFQGFVVGDWNGHGQVPGCSNTDCPASINAGVDMLMAPDSWRGLYEHTLA 366

Query: 372 QARDGTLPIDRLDDAVRRILRVKIRAGLFEAGKPSSRPYAGR-YELLGSAEHRALAREAV 430
           +A+ G +P  RLDDAV RILRVK R GLFEAG PS++P A +  E++GSA HRALAR AV
Sbjct: 367 EAKSGAIPAARLDDAVARILRVKFRLGLFEAGAPSTQPLATKSAEVIGSAAHRALARRAV 426

Query: 431 RQSLVLLKNANGLLPLKPGGRILVAGDGADNLTKQTGGWTLSWQGTGTQRSDFPNAQSIW 490
           R+SLVLLKN +G+LPL P   ILVAGD ADN+++Q+GGWTL+WQGTG    DFP AQSI 
Sbjct: 427 RESLVLLKNNHGVLPLDPRKHILVAGDAADNISRQSGGWTLTWQGTGLGNKDFPGAQSIG 486

Query: 491 EGIEATVKAAGGTATLSVEGGYSAKPDAAIVVFGEEPYAEFQGDRPDVGY--DDAKTLAL 548
            GI   VKAAGG   ++ +G Y+ KPD A+VVFGE+PYAEFQGD P++ Y   D   L L
Sbjct: 487 AGIAEQVKAAGGQVEIAADGRYTNKPDVAVVVFGEDPYAEFQGDLPNLLYRPGDEHDLEL 546

Query: 549 LRTLKTAGVPTVAVFLSGRAMWVNPFLNASDAFVAAWLPGSEGGGVADVLFGK------S 602
           LR L   G+P VAVFLSGR +WVN  +N +DAFVAAWLPGSEGGGVADVL  K      +
Sbjct: 547 LRRLHGDGIPVVAVFLSGRPLWVNREINVADAFVAAWLPGSEGGGVADVLLRKRDGKIAN 606

Query: 603 DFSGKLGYSWPRSSDQTTVNIGDSNYDPLFPYGFGLKVADRGDLAALPETRA-TAAAAET 661
           DF GKL Y+WP S        G+S     FP+G+GL+ AD  +   LPE    T      
Sbjct: 607 DFHGKLAYAWPGSG---VHGQGESR----FPFGYGLRYADHAEALDLPEASGITGEQIPV 659

Query: 662 GILFTAGKPGGGRRL-LLGRPGELAANPGPE------LIDARPADRSAQEDSLRIRWTGA 714
           G     GK   G    LLG  G   A    +       +     D  AQED+ R  W   
Sbjct: 660 GNYLERGKSVRGYTFRLLGADGVAVAGDTSKSGTADGSLRMSALDYKAQEDARRFEWKKN 719

Query: 715 GQAVAAIVQDVPVDLSRQANGDLALELELKVNAAPSAEVSLLMRCGTDCAGGFPVRGILG 774
           G A  AI    P DL RQ NGD+ L   L+V+A P  +  + M CG  C G   +   L 
Sbjct: 720 G-AELAIQSRAPFDLDRQTNGDVLLVTTLRVDALPGKDAWIGMGCGAGCKGRVNLGPTL- 777

Query: 775 EAAKTGKWTRVAVPLRCFEKAGVDMTRVETPLSIATAGSLDLTLSSARITSPSGPQLAC 833
            +   G WTRV VPL+CF  AG DM R++ P          L L+   + + +   + C
Sbjct: 778 TSLPAGTWTRVGVPLKCFRTAGADMHRIDQPFVWGAGAGSSLALARVALGTDADQVVDC 836


Lambda     K      H
   0.317    0.135    0.412 

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: 2066
Number of extensions: 117
Number of successful extensions: 8
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: 834
Length of database: 838
Length adjustment: 42
Effective length of query: 792
Effective length of database: 796
Effective search space:   630432
Effective search space used:   630432
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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