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

GapMind for catabolism of small carbon sources

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

Align Alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate N515DRAFT_3393 N515DRAFT_3393 alpha-glucosidase

Query= reanno::ANA3:7025148
         (540 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3393
          Length = 541

 Score =  744 bits (1922), Expect = 0.0
 Identities = 350/522 (67%), Positives = 407/522 (77%), Gaps = 9/522 (1%)

Query: 1   MSELTWWRGAVIYQIYPRSLLDTNGDGVGDLRGIITKLDYIASLNVDAIWISPFFKSPMA 60
           MSE  WWRGAVIYQIYPRS LDT+GDGVGDL GI+ +LDYIA L VDAIWI+PFF+SPMA
Sbjct: 1   MSETPWWRGAVIYQIYPRSFLDTDGDGVGDLPGIVERLDYIAGLGVDAIWIAPFFRSPMA 60

Query: 61  DFGYDISDYREVDPLFGTMQDFDELIEKAHQRGIKVIIDQVLSHTSDQHAWFCESRESRT 120
           DFGYDI+DYR VDPLFGT+ DFD L+ KAH  G+KV+IDQVLSHTSDQH WF ESR SR 
Sbjct: 61  DFGYDIADYRAVDPLFGTIDDFDRLLAKAHALGLKVMIDQVLSHTSDQHEWFKESRASRD 120

Query: 121 NPKADWYVWAEPKEDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLRSQPDINFHNPDVR 180
           NPKADWYVWA+ ++DGT PNNW+++FGG AW+WEPRR QYYLHNFL SQPD+NFH+PDV+
Sbjct: 121 NPKADWYVWADARDDGTPPNNWMSLFGGVAWQWEPRRGQYYLHNFLTSQPDLNFHHPDVQ 180

Query: 181 QAVLDNVEFWLKKGVDGFRLDAITFCYHDEQLRDNPPKPKDKRQGRGFSEDNPYAYQYHY 240
           +AVLDNV+FWL KGVDG RLDAI FC+HD QLRDNPPKP+  R GRGFS DNPYA+QYHY
Sbjct: 181 RAVLDNVQFWLDKGVDGLRLDAINFCFHDRQLRDNPPKPQAMRVGRGFSPDNPYAFQYHY 240

Query: 241 YNNDRPQTILFIEELRQLINRYPGAVTLGEVSAEDSLAVMAAYTKGEDRLHMAYSFELLT 300
           YNN +P+ + F+EELR L++RYPGA  LGE+S+EDSLA MA YT G  RLHM YSFELLT
Sbjct: 241 YNNTQPENLAFLEELRGLLDRYPGAAALGEISSEDSLATMAEYTTGH-RLHMGYSFELLT 299

Query: 301 DDYSAAYIRQTVEALEASIGDGWPCWAIGNHDAQRVASRWGR-----GKQTSDMVKMLNA 355
            D+SAAYIR TVE LEA + +GWPCWAI NHD +RV SRWGR     G  +  +  +L A
Sbjct: 300 ADFSAAYIRGTVERLEAQMTEGWPCWAISNHDVERVLSRWGREARGNGDASVRLANLLTA 359

Query: 356 MVNSLRGSVCSYQGEELGLTEAPIEYHELQDPFGKTFWPMFKGRDGCRTPMPWEQNADFS 415
           MV SLRGSVC YQGEEL LTEA + Y  LQDP+G TFWP FKGRDGCRTPMPW+++A+ +
Sbjct: 360 MVCSLRGSVCVYQGEELALTEAEVPYEALQDPYGITFWPNFKGRDGCRTPMPWDESAN-A 418

Query: 416 GFSQVTPWLPIAQAHRALAVDVQEADSQSMLHGYRQFLAWRKGYPALVEGEIEFLDAPEP 475
           GFS   PWLP+   HRALAV  QE D  S LHG+R F+ WR+  P L  G I FLD PEP
Sbjct: 419 GFSSGAPWLPVPAGHRALAVSRQELDPASALHGFRGFMQWRQAQPELRWGAIGFLDTPEP 478

Query: 476 LLVFVRTSGEQKLLVCFNLQDTEQALSLDALSIQQEITGHGL 517
           +L F RT   + +L  FNL     A++L      + I GHGL
Sbjct: 479 VLAFTRTHAGETVLAAFNLGSAPVAVALPLAG--ERIGGHGL 518


Lambda     K      H
   0.320    0.137    0.436 

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: 1027
Number of extensions: 33
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: 540
Length of database: 541
Length adjustment: 35
Effective length of query: 505
Effective length of database: 506
Effective search space:   255530
Effective search space used:   255530
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 (21.8 bits)
S2: 52 (24.6 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