GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligU in Shewanella amazonensis SB2B

Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate 6939203 Sama_3297 hypothetical protein (RefSeq)

Query= SwissProt::Q88JY0
         (361 letters)



>FitnessBrowser__SB2B:6939203
          Length = 396

 Score =  196 bits (498), Expect = 9e-55
 Identities = 141/391 (36%), Positives = 196/391 (50%), Gaps = 48/391 (12%)

Query: 3   QTRIPCLLMRGGTSKGAYFLHDDLP----APGPLRDRVLLAVMGSPD--ARQIDGIGGAD 56
           Q RIP   MRGGTSKG +F  DDLP     PG  RD +LL V+GSPD   +  DG+GGA 
Sbjct: 5   QIRIPATYMRGGTSKGVFFRLDDLPEAARVPGAERDALLLRVIGSPDPYGKHTDGMGGAT 64

Query: 57  SLTSKVAIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAAS- 115
           S TSK  I+  S     DVDYL+ QV +D A VD+  NCGN+    G FA+  GLV AS 
Sbjct: 65  SSTSKCVIMNKSSVPGHDVDYLYGQVSIDTAFVDWSGNCGNLSTAAGAFAIHAGLVDASR 124

Query: 116 ---GASTPVRIFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVA--G 170
                   VRI+  N G+  +A VP  +G+V+  GD  +DGV   AA +V+ F D A  G
Sbjct: 125 VPENGICEVRIWQANIGKTIIAHVPVTNGEVQETGDFELDGVTFPAAEIVLEFVDPADDG 184

Query: 171 ASCGALLPTGNSRDCVE---------GVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEA 221
              GA+ PTGN  D +E          +  T I+ G+P + + AEDLG  G E  E +  
Sbjct: 185 EDGGAMFPTGNLVDELEVPSEVHPSGKIRATLINAGIPTIFVNAEDLGYRGDELQEAING 244

Query: 222 DSALKTRLEAIRLQLGPRMNLGDV-----SQRNVPKMCLLSAP-----RNGGTVN----- 266
           +       E +R     RM L        ++++ PK+  ++ P      +G TV      
Sbjct: 245 NPVALAMFEQLRAHGAIRMGLIKTLDEAKTRQHTPKVAFVTNPMTHVVSSGKTVAEDEVD 304

Query: 267 --TRSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLASTSGGDRQRLAVEHPSGEFTVE 324
              R+    + H ++    AV++ TA  I G++     +  GG+RQ +   HPSG  T+ 
Sbjct: 305 LLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVN--LAAGGGERQAVRFGHPSG--TLR 360

Query: 325 ISLEHGVIKGCGLV------RTARLLFDGVV 349
           +  E   + G   V      R+AR+L +G V
Sbjct: 361 VGAEAKQVDGQWTVTKAIMSRSARILMEGTV 391


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: 418
Number of extensions: 30
Number of successful extensions: 7
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: 396
Length adjustment: 30
Effective length of query: 331
Effective length of database: 366
Effective search space:   121146
Effective search space used:   121146
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: 50 (23.9 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