GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligU in Magnetospirillum magneticum AMB-1

Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate WP_011382697.1 AMB_RS01270 4-oxalomesaconate tautomerase

Query= SwissProt::Q88JY0
         (361 letters)



>NCBI__GCF_000009985.1:WP_011382697.1
          Length = 363

 Score =  384 bits (987), Expect = e-111
 Identities = 198/359 (55%), Positives = 245/359 (68%), Gaps = 3/359 (0%)

Query: 3   QTRIPCLLMRGGTSKGAYFLHDDLPAPGPLRDRVLLAVMGSPDARQIDGIGGADSLTSKV 62
           QT IPCL MRGGTS+G +FL  DLPA   LRD+VLLAVMGSP ARQIDG+GG   LTSKV
Sbjct: 2   QTPIPCLFMRGGTSRGPFFLESDLPADMALRDKVLLAVMGSPHARQIDGLGGGHPLTSKV 61

Query: 63  AIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASGASTPVR 122
            I+R S     D+D+LFAQ+  D   VD   NCGN+LA V PFALERG+V   G +T +R
Sbjct: 62  GIVRPSTTPGVDLDFLFAQLQPDRETVDTTPNCGNMLAAVVPFALERGIVRPQGDTTTLR 121

Query: 123 IFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAGASCGALLPTGNS 182
           +   NT       V T  G++EY G+ RIDGVPG A+ + + F D AG+ C  LLPTG +
Sbjct: 122 VLTLNTDMQCDITVRTPGGRMEYQGEARIDGVPGTASPIAINFLDTAGSVCTGLLPTGRT 181

Query: 183 RDCVEGVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSALKTRLEAIRLQLGPRMNL 242
           RD ++G+EVTCIDNGMP+VL  A DLG TG E  ETL AD+ LK R+E +RL+ G  M L
Sbjct: 182 RDVIDGLEVTCIDNGMPMVLFRAADLGRTGAESVETLNADTELKARIETLRLKAGHLMGL 241

Query: 243 GDVSQRNVPKMCLLSAPRNGGTVNTRSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLA 302
           GDV  +N PKMCL++ P  GG + TR FIPH CH +IGV  AV+VATAC++EGSV +GLA
Sbjct: 242 GDVGPKNYPKMCLVAPPSAGGALGTRCFIPHVCHDAIGVLAAVTVATACVLEGSVTEGLA 301

Query: 303 STSGGDRQRLAVEHPSGEFTVEISLEHG---VIKGCGLVRTARLLFDGVVCIGRDTWGG 358
           +  GG  + +AVEHP+GEF+VE+ L+      +    L+RTARLL  G V I    W G
Sbjct: 302 NVPGGAVKTIAVEHPTGEFSVELELDLADPQKVVRAALLRTARLLMKGEVMIPAAIWEG 360


Lambda     K      H
   0.320    0.138    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: 454
Number of extensions: 18
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: 361
Length of database: 363
Length adjustment: 29
Effective length of query: 332
Effective length of database: 334
Effective search space:   110888
Effective search space used:   110888
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: 49 (23.5 bits)

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

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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:

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:

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:

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:

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