Alignments for a candidate for xacD in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Sinorhizobium meliloti 1021

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate SMc00884 SMc00884 dihydroxy-acid dehydratase

Query= reanno::Smeli:SM_b20890
         (579 letters)



>FitnessBrowser__Smeli:SMc00884
          Length = 574

 Score =  739 bits (1909), Expect = 0.0
 Identities = 371/571 (64%), Positives = 445/571 (77%), Gaps = 2/571 (0%)

Query: 9   RKLRSQEWFGGTGKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAE 68
           ++LRS+ W+GGT K+  +HRSWMKNQG P   FDGRPIIGICNTWSELTPCN+HLR LAE
Sbjct: 6   KELRSRHWYGGTHKDGFIHRSWMKNQGFPDHVFDGRPIIGICNTWSELTPCNSHLRILAE 65

Query: 69  RVKRGVYEAGGFPVEFPVFSTGESTLRPTAMMFRNLAAMDVEESIRGNPVDGVVLLGGCD 128
            VKRGV+EAGGFPVEFPV S GE+ +RPTAM+FRNL AMDVEE+IR   +DGVVLLGGCD
Sbjct: 66  GVKRGVWEAGGFPVEFPVSSLGETQMRPTAMLFRNLLAMDVEEAIRAYGIDGVVLLGGCD 125

Query: 129 KTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMD 188
           KTTP  LMGAASVD+P IVVS GPMLNGKW+GKD+GSGT +W+FSE V++GEMSL+EFM 
Sbjct: 126 KTTPGQLMGAASVDLPTIVVSSGPMLNGKWKGKDIGSGTDVWKFSEAVRAGEMSLQEFMA 185

Query: 189 AEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMV 248
           AE GM+RS G CMTMGTA+TMAS+ EA+G++L  NAA+PAVDARR  +S +TG+RIVEMV
Sbjct: 186 AESGMSRSPGVCMTMGTATTMASIVEAMGLSLPTNAALPAVDARRMALSHMTGKRIVEMV 245

Query: 249 KEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPT 308
            EDL+ S ILTKE FEN I  N AVGGSTNAV+H+LA+AGR G+DL L+D+DR+G  VP 
Sbjct: 246 HEDLRLSKILTKENFENGIIANAAVGGSTNAVVHMLAIAGRAGIDLCLEDFDRVGGQVPC 305

Query: 309 IVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKGVVNYNEDV 368
           IVN  PSGKYL+E+  YAGGLP V+  +    LLH DA TV G  I    +    YN+DV
Sbjct: 306 IVNCMPSGKYLIEDLAYAGGLPAVMNRIQH--LLHPDAPTVFGVPISKYWEAAEVYNDDV 363

Query: 369 ILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINRE 428
           I P +  L  + GI VL+GNLAP GAV+KPSAAS HL+ H+G A VF++IED  A+I+  
Sbjct: 364 IRPLDNPLRAAAGIRVLKGNLAPNGAVIKPSAASEHLLAHEGPAYVFDTIEDLRAKIDDP 423

Query: 429 DLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIRISDARMSGTAYGTVI 488
           DL + E  I+VLK CGPKGYPGMAEVGNM +P ++++KG+ DM+RISDARMSGTA+GTV+
Sbjct: 424 DLPVTEDTILVLKGCGPKGYPGMAEVGNMPIPRRLVEKGVRDMVRISDARMSGTAFGTVV 483

Query: 489 LHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGG 548
           LH +PEA  GGPLA+V  GD I +D     L+L VS+EELA R AAW  P +    GY  
Sbjct: 484 LHVSPEANAGGPLAIVRTGDRIRLDALKGELNLLVSEEELAARMAAWQPPEQKWHRGYYK 543

Query: 549 LYIKTVMQADAGADLDFLVGARGSVVERDSH 579
           LY  TV+QAD GADLDFLVG  GS V R+SH
Sbjct: 544 LYHDTVLQADKGADLDFLVGKSGSEVLRESH 574


Lambda     K      H
   0.318    0.135    0.402 

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: 1079
Number of extensions: 61
Number of successful extensions: 2
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: 579
Length of database: 574
Length adjustment: 36
Effective length of query: 543
Effective length of database: 538
Effective search space:   292134
Effective search space used:   292134
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