Alignments for a candidate for uxaA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxaA in Echinicola vietnamensis KMM 6221, DSM 17526

Align Altronate dehydratase (EC 4.2.1.7) (characterized)
to candidate Echvi_3632 Echvi_3632 Altronate dehydratase

Query= reanno::Pedo557:CA265_RS19875
         (548 letters)



>FitnessBrowser__Cola:Echvi_3632
          Length = 548

 Score =  647 bits (1669), Expect = 0.0
 Identities = 322/552 (58%), Positives = 407/552 (73%), Gaps = 8/552 (1%)

Query: 1   MVTRILKIHPNDNVLVALQNLAKGETVIYDGHEYILQDDIQAKHKFFMQDMNAGDHIIMY 60
           M+ +ILKIHP DNVLVAL +L  GE + ++G+E  L  D++AKHKF        + I MY
Sbjct: 1   MLHKILKIHPKDNVLVALTDLKAGEQIEFEGNEITLTHDVKAKHKFAEAAFATDEDIYMY 60

Query: 61  GVLVGKAQHFILKGGLMDTENTKHASDPY----EFRPYHYEWHAPDVSKFEGRTFNGYIR 116
           G++ GKA + I KG ++ T+N  H +  +    +F+P    W+APDVSK+  RTF GY R
Sbjct: 61  GIICGKAMNAIAKGEVLTTQNVAHKTSEFTGVRDFKP----WNAPDVSKWADRTFMGYHR 116

Query: 117 SDGRVGTANYWLFIPTVFCENRNLDVIREALHNELGYAVTDKYKSYAHQLVEAYKNGEIL 176
            DG+VGTANYWL IP VFCENRN+++++ A   ELG+A  +KYKS+  Q+ + Y  G+  
Sbjct: 117 EDGQVGTANYWLVIPLVFCENRNIEIMKNAFVEELGFAKPNKYKSFVKQMKDLYTQGKKE 176

Query: 177 AEADPSSIGLANPSANRVFKNVDGIKFLNHQGGCGGTRQDAAVLSKLLAAYADHPNVAGV 236
             A  S         +R+FKN+DGIKFL HQ GCGG RQD+ +L  L+A Y ++PNVAG 
Sbjct: 177 EIATLSVETAEQDGESRIFKNIDGIKFLTHQAGCGGIRQDSEMLCGLIAGYINNPNVAGA 236

Query: 237 TVLSLGCQNLQVKDFMDDLKHRSPNFDKPLFVFEQQQSQSEEQLVKEAIRKTFIGLTEIN 296
           T+LSLGCQN Q     + L   +P+  KP+ + EQQQ  +E  L+  AI+KTF+ LT+ +
Sbjct: 237 TILSLGCQNAQPSILREKLDKINPDLKKPVIILEQQQEGTENTLLTNAIQKTFLALTDAD 296

Query: 297 KIERQPAPLSKLVLGVKCGGSDGFSGISANPAVGYTSDLLVALGGTVLLAEFPELCGAEQ 356
           ++ERQPAPLSKL +G++CGGSDGFSGISANP+VG+ SDL+VALGG  +L+EFPELCG EQ
Sbjct: 297 QLERQPAPLSKLTVGLECGGSDGFSGISANPSVGHASDLVVALGGKTILSEFPELCGVEQ 356

Query: 357 QLIDRTKDETAARKFIQLMTAYNQSAENVGSGFFMNPSPGNIKDGLITDAIKSTGAAKKG 416
           +LI+R   + +A KF+ LM AY  SAE VGSGF MNPSPGNIKDGLITDA+KS GAAKKG
Sbjct: 357 ELINRCTTDESADKFVTLMRAYAASAEAVGSGFDMNPSPGNIKDGLITDAMKSAGAAKKG 416

Query: 417 GTSPVEDVLDYTEPATKPGLNLVCTPGNDVEATTGKAASGATLILFTTGLGTPTGNPVCP 476
           GTSP+ DVLDY E  TKPGLNL+CTPGNDVE+TT  A SGA +ILFTTGLGTPTGNPV P
Sbjct: 417 GTSPIVDVLDYAEYVTKPGLNLLCTPGNDVESTTAMAGSGANVILFTTGLGTPTGNPVTP 476

Query: 477 TIKVSTNNALTKRMGDIIDINCGPVIEGEKTIEQMGEDILEYCIKAASGEVIPKAVLLNQ 536
            +KVS+N+ L ++M DIIDIN G VI G+KTI+QMGE+ILE+ I+ ASG    KA+ LNQ
Sbjct: 477 VLKVSSNHILAEKMDDIIDINTGGVISGDKTIDQMGEEILEHIIEVASGNKKAKAMTLNQ 536

Query: 537 DDFIPWKRGVSL 548
           DDFIPWKRGVSL
Sbjct: 537 DDFIPWKRGVSL 548


Lambda     K      H
   0.317    0.136    0.400 

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: 924
Number of extensions: 39
Number of successful extensions: 3
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: 548
Length of database: 548
Length adjustment: 36
Effective length of query: 512
Effective length of database: 512
Effective search space:   262144
Effective search space used:   262144
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: 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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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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