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

GapMind for catabolism of small carbon sources

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

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate N515DRAFT_2409 N515DRAFT_2409 dihydroxy-acid dehydratase

Query= reanno::BFirm:BPHYT_RS19730
         (577 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2409
          Length = 574

 Score =  835 bits (2157), Expect = 0.0
 Identities = 416/572 (72%), Positives = 485/572 (84%), Gaps = 4/572 (0%)

Query: 8   KKPLR-SQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFREL 66
           KKPLR SQ WFG + + GF +RSW+K  G+P+D FDGRPVIGICNTWSELTPCN+ FREL
Sbjct: 5   KKPLRRSQEWFGREGKQGFYYRSWLKGLGLPNDMFDGRPVIGICNTWSELTPCNSSFREL 64

Query: 67  AEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVG 126
           AE+VK+GV+EAGG PLEFPVMSLGET +RPTAMLFRNLASMDVEESIR NP+DGV+LL+G
Sbjct: 65  AEHVKRGVYEAGGFPLEFPVMSLGETQMRPTAMLFRNLASMDVEESIRANPIDGVVLLMG 124

Query: 127 CDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEEF 186
           CDKTTPAL+MGAAS NLP + +SGGP L+G +RG+ IGSGTGV +MSE VRAG + QEEF
Sbjct: 125 CDKTTPALMMGAASVNLPTIGLSGGPSLSGNWRGQPIGSGTGVIRMSEMVRAGELAQEEF 184

Query: 187 TEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVD 246
            EAE+CM RS+G CMTMGTASTMASMVE+LG+ LP NAAIPAVD+RR  LAHL+GRRIV+
Sbjct: 185 VEAEACMQRSKGSCMTMGTASTMASMVEALGLSLPENAAIPAVDSRRFRLAHLSGRRIVE 244

Query: 247 MVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE-LGSNV 305
           MV EDL M KILTR AFENAIR NAAIGGSTNAV+HL+ALA R+GVEL+L+DW+ LGS++
Sbjct: 245 MVHEDLRMSKILTRAAFENAIRANAAIGGSTNAVIHLLALAGRLGVELALDDWDRLGSHL 304

Query: 306 PCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYDE 365
           PCLVNL+PSG+YLMEDFYYAGGLPAVL+++     LH  ALT NG+TL DN+  A  ++ 
Sbjct: 305 PCLVNLKPSGDYLMEDFYYAGGLPAVLREIAPH--LHLGALTANGRTLGDNIATAPCWNR 362

Query: 366 KVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKID 425
            VI    EP K +AGIAVL+GNLAP+GAVIKPSAA+A LL+HRGRAVVFENI++  A+ID
Sbjct: 363 DVIRPIEEPLKREAGIAVLRGNLAPDGAVIKPSAASAHLLQHRGRAVVFENIDDFKARID 422

Query: 426 DESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTAYGA 485
           DE+LDIDE C+MVLK  GP+GYPG AEVGNMPLP K+L++GITD+VRISD RMSGTAYG 
Sbjct: 423 DEALDIDETCVMVLKNCGPRGYPGMAEVGNMPLPPKLLRRGITDIVRISDARMSGTAYGT 482

Query: 486 VVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAPKRGYY 545
           VVLH SPEAAAGG LA V+ GD IELDV  RRLHLD+ D+ELARRRAAW+AP  P+RG+ 
Sbjct: 483 VVLHASPEAAAGGNLALVRDGDFIELDVPGRRLHLDLADDELARRRAAWKAPPPPERGWA 542

Query: 546 KLYVEHVLQADQGADLDFLVGSSGAPVPRDSH 577
           KLYV+HV QA  GADLD LVG SG+ V  DSH
Sbjct: 543 KLYVDHVQQAHLGADLDILVGGSGSDVAGDSH 574


Lambda     K      H
   0.318    0.135    0.401 

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: 1169
Number of extensions: 48
Number of successful extensions: 5
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: 577
Length of database: 574
Length adjustment: 36
Effective length of query: 541
Effective length of database: 538
Effective search space:   291058
Effective search space used:   291058
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 (21.7 bits)
S2: 53 (25.0 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