GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SB2B:6939203 Sama_3297 hypothetical protein
           (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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